Anti-inflammatory compounds and methods of use

ABSTRACT

Methods of treating or inhibiting inflammation in a subject include administering an anti-inflammatory protein to the subject. In some embodiments, the protein has at least 80% sequence identity to the amino acid sequence set forth as SEQ ID NO: 1, SEQ ID NO: 17, or fragments thereof. Isolated polypeptides, nucleic acids, and recombinant vectors including a nucleic acid encoding the anti-inflammatory protein (such as a nucleic acid encoding a protein with at least 80% sequence identity to SEQ ID NO: 1, SEQ ID NO: 17, or fragments thereof) operably linked to a heterologous promoter are also disclosed.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a continuation-in-part of U.S. application Ser. No.15/311,667, filed Nov. 16, 2016, which is the § 371 U.S. National Stageof International Application No. PCT/US2015/031052, filed May 15, 2015,which was published in English under PCT Article 21(2), which in turnclaims the benefit of U.S. Provisional Application No. 61/994,601, filedMay 16, 2014, all of which are incorporated herein by reference in theirentirety.

ACKNOWLEDGMENT OF GOVERNMENT SUPPORT

This invention was made with government support under grants R01GM095385, P50GM098911-01A1, 1F32DK098884-01A1, P01 HD022486, andR01CA176579, awarded by the National Institutes of Health. Thegovernment has certain rights in the invention.

FIELD

This disclosure relates to anti-inflammatory proteins from gutmicrobiota and methods of their use.

BACKGROUND

Inflammatory disorders such as allergies, asthma, rheumatoid arthritis,inflammatory bowel disease, and atherosclerosis affect large numbers ofpeople. While anti-inflammatory drugs are available, many have seriousside effects, including increased risk of stroke or gastric damage orare systemic suppressors of the immune system. Thus, there remains aneed for additional anti-inflammatory therapies.

SUMMARY

The inventors have identified a protein from Aeromonas withanti-inflammatory activity (referred to herein in some examples asanti-inflammatory protein (AP), protein 1882, or AimA, for example, SEQID NO: 1). Disclosed herein are methods of treating or inhibiting (forexample, reducing) inflammation in a subject by administering the newlyidentified anti-inflammatory protein to a subject. In some embodiments,the protein has at least 80% sequence identity to the amino acidsequence set forth as SEQ ID NO: 1 or fragments thereof. In someexamples, the subject has an inflammatory disease, such as inflammatorybowel disease, rheumatoid arthritis, osteoarthritis, inflammatory lungdisease, atherosclerosis, systemic lupus erythematosus, Sjogren'ssyndrome, asthma, allergic rhinitis, psoriasis, irritable bowelsyndrome, necrotizing enterocolitis, or atopy. In other embodiments, theprotein (such as a polypeptide with at least 80% sequence identity toSEQ ID NO: 1 is used in methods of treating or inhibiting sepsis orseptic shock in a subject.

Also disclosed herein are methods of identifying anti-inflammatorycompounds by determining the effect of test compounds on one or moremarkers of inflammation (for example, neutrophil accumulation inzebrafish gut). In some embodiments, germ-free zebrafish or zebrafishinoculated with a single defined bacterial strain (or a definedcombination of strains) are contacted with one or more test compoundsand the number of neutrophils in the gut of the zebrafish are measuredand compared to a control. In one specific example, the zebrafish is atransgenic zebrafish expressing a fluorescent protein (e.g., greenfluorescent protein (GFP)) or another marker under the control of theneutrophil-specific myeloperoxidase (MPO) promoter. This system permitsmeasurement of neutrophil accumulation in the gut of living organisms.

Recombinant vectors including a nucleic acid encoding the hereinidentified anti-inflammatory protein (such as a nucleic acid encoding aprotein with at least 80% sequence identity to SEQ ID NO: 1 or afragment thereof) operably linked to a heterologous promoter are alsodisclosed. In some examples, the nucleic acid encoding the protein isset forth in SEQ ID NO: 2. Cells including the recombinant vector (forexample, cells transformed with the vector) are also disclosed.

Also disclosed herein are isolated polypeptides with at least 80%sequence identity (such as at least 85%, 90%, 95%, or even 100%identity) to the amino acid sequence of SEQ ID NO: 11, an amino acidsequence 130-190 amino acids in length with at least 80% sequenceidentity (such as at least 85%, 90%, 95%, or even 100% identity) toamino acids 1-188 of SEQ ID NO: 11, amino acids 21-188 of SEQ ID NO: 11,or amino acids 189-330 of SEQ ID NO: 11, or an amino acid sequence120-180 amino acids in length with at least 80% sequence identity (suchas at least 85%, 90%, 95%, or even 100% identity) to amino acids 1-185of SEQ ID NO: 1, amino acids 23-185 of SEQ ID NO: 1, or amino acids192-313 of SEQ ID NO: 1. The polypeptides may be used in treating orinhibiting inflammation or sepsis or septic shock in a subject.

Also disclosed are isolated nucleic acids with at least 80% sequenceidentity (such as at least 85%, 90%, 95%, or even 100% identity) to thenucleic acid sequence of SEQ ID NO: 17, a nucleic acid 360-540nucleotides in length and having at least 80% sequence identity (such asat least 85%, 90%, 95%, or even 100% identity) to nucleotides 1-564 ofSEQ ID NO: 17, nucleotides 61-564 of SEQ ID NO: 17, or nucleotides565-990 of SEQ ID NO: 17, or a nucleic acid 360-540 nucleotides inlength with at least 80% sequence identity (such as at least 85%, 90%,95%, or even 100% identity) to nucleotides 1-555 of SEQ ID NO: 2,nucleotides 67-555 of SEQ ID NO: 2, or nucleotides 574-939 of SEQ ID NO:2. In some embodiments, the nucleic acids are operably linked to apromoter, for example, in a recombinant vector. Also disclosed are cellscomprising the recombinant vector or transformed cells including one ormore of the nucleic acids operably linked to a promoter.

The foregoing and other features of the disclosure will become moreapparent from the following detailed description, which proceeds withreference to the accompanying figures.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a graph showing the number of myeloperoxidase (MPO) positivecells in the gut of zebrafish raised germ-free (GF), conventionally(CVZ), mono-associated with type II secretion system (T2SS) deletionmutant A. veronii (Leech AMA DT2SS), and mono-associated with wild-type(WT) Aeromonas veronii (Leech AMA). A and B indicate groups that aresignificantly different from one another (ANOVA, p<0.05).

FIG. 2 is a graph showing the number of MPO positive cells in the gut ofzebrafish raised GF, CVZ, mono-associated with DT2SS A. veronii (LeechAMA DT2SS), mono-associated with WT A. veronii (Leech AMA), ormono-associated with DT2SS A. veronii and cell-free supernatant (CFS)from WT A. veronii (DT2SS+WT CFS) or from DT2SS A. veronii (DT2SS+DT2SSCFS). A and B indicate groups that are significantly different from oneanother (ANOVA, p<0.05). The first four lanes repeat data shown in FIG.1, for the sake of comparison.

FIG. 3 is a digital image of Coomassie-blue stained SDS-PAGE of A.veronii CFS fractions. Lane 1: ladder; lane 2: concentrated CFS; lane 3:empty; lane 4: 0-20% ammonium sulfate fraction; lane 5: empty; lane 6:20-40% ammonium sulfate fraction; lane 7: empty; lane 8: 40-60% ammoniumsulfate fraction.

FIG. 4 is a graph showing the number of MPO positive cells in the gut ofzebrafish raised GF, CVZ, mono-associated with DT2SS A. veronii (LeechAMA DT2SS), mono-associated with WT A. veronii (Leech AMA),mono-associated with DT2SS A. veronii and CFS from WT A. veronii(DT2SS+WT CFS), mono-associated with DT2SS A. veronii and CFS from DT2SSA. veronii (DT2SS+DT2SS CFS), mono-associated with DT2SS A. veronii plus0-20% ammonium sulfate fraction, (0-20), mono-associated with DT2SS A.veronii plus 20-40% ammonium sulfate fraction (20-40), ormono-associated with DT2SS A. veronii plus 40-60% ammonium sulfatefraction (40-60). A and B indicate groups that are significantlydifferent (ANOVA, p<0.05). The first six lanes repeat data shown in FIG.2, for the sake of comparison.

FIG. 5A is a graph showing the number of MPO positive cells in the gutof zebrafish raised GF, CVZ, mono-associated with DT2SS A. veronii(Leech AMA DT2SS), mono-associated with WT A. veronii (Leech AMA),mono-associated with DT2SS A. veronii plus CFS from WT A. veronii(DT2SS+WT CFS), or mono-associated with DT2SS A. veronii plus CFS fromDT2SS A. veronii (DT2SS+DT2SS CFS). The graph also shows zebrafishtransgenic for MPO:GFP or WT fish mono-associated with DT2SS A. veroniiplus CFS from E. coli carrying a control plasmid (DT2SS+EV),mono-associated with DT2SS A. veronii plus CFS from E. coli carrying aplasmid for chitin binding protein (dT2SS+CBP), or mono-associated withDT2SS A. veronii plus CFS from E. coli carrying a plasmid with the genefor AP (dT2SS+1882). A and B indicate groups that are significantlydifferent (ANOVA, p<0.05). * indicates significantly different between+EV condition and +AP (1882) condition.

FIG. 5B is a diagram showing the E. coli expression vectors for AP andCBP proteins. Expression is induced with IPTG. RBS, ribosome bindingsite; MCS, multiple cloning site; EV, empty vector.

FIG. 6 is a graph showing the number of MPO positive cells in the gut ofzebrafish infected with Vibrio (Vib: 48 hours of Vibrio infection),zebrafish infected with Vibrio treated with CFS from E. coli carrying acontrol plasmid (Vib+EV), zebrafish infected with Vibrio treated withCFS from E. coli carrying a plasmid with the gene for AP under aninducible promoter (Vib+1882), or GF. *: p<0.05; NS: not significant.

FIG. 7A is a schematic showing A. veronii AP (hatched line) andconserved structural domains compared to known proteins. The N-terminalregion of A. veronii AP shows similarity to secretion signal sequencesfrom other proteins. The main conserved domain (3pnq_A) has similarityto decaheme cytochrome C from Shewanella oneidensis. The protein alsoincludes a beta-trefoil domain (2vxt_I) that is also found in thecytokine superfamily (such as IL-18 and IL-1b).

FIG. 7B is a diagram illustrating interleukin-1 (IL-1) signaling pathwayand a proposed role for AP in blocking IL-1R1 signaling. The inset showsphylogenetic relationship of the AP β-trefoil domain (BTD) to the samedomain from the indicated human (h), mouse (m), zebrafish (z), salmon(sal), and catfish (cf) proteins. The sequences used in constructing thephylogenetic tree are as follows (GenBank Accession Nos.): zfIL1β,NP_998009.2; zfIL1ra, AEJ36293.1; hIL1β, NP_000567.1; mIL1β, AAH11437.1;hIL1ra, AAH09745.1; mIL1ra, AAA39278.1; hIL1α, CAG33695.1; mIL1α,AAH03727.1; cfIL1β, NP_001187149; and salIL1β, NP_0011178191. AP BTDused in generating the phylogenetic tree was amino acids 148-176 of SEQID NO: 1.

FIG. 8 is a digital image of a Coomassie-blue stained gel showingsupernatant from cultures of E. coli carrying a control plasmid (emptyvector) or a plasmid with the AP gene (AP) or the chitin binding proteingene (CBP).

FIGS. 9A-9D are a series of graphs showing sox10 zebrafishcharacteristics and the effect of inoculating germ-free fish withmicrobiota from sox10 fish. FIG. 9A is a graph showing bacterial load inWT and sox10 fish. FIG. 9B is a graph showing diversity of the bacterialcommunities in WT and sox10 fish. FIG. 9C is a graph showing neutrophilinflux to the intestine in WT and sox10 fish. FIG. 9D is a graph showingneutrophil influx to the intestine in WT GF zebrafish inoculated witheither microbiota from a WT or a sox10 donor fish. **p<0.01, ***p<0.001,T test.

FIG. 10 is a graph showing neutrophil influx in WT or sox10 zebrafishtreated with empty vector (EV), 0.5 μg/ml CFS from E. coli expressing APprotein, or 1 μg/ml CFS from E. coli expressing AP protein. *p<0.05.

FIG. 11 is a graph showing the effect of infection of WT zebrafish withA. veronii Hm21 or Hm21 ΔAP on inflammation (neutrophil influx in theintestine). The graph shows percent of inoculated fish with severe(black), mild (gray), or no (white) inflammation.

FIG. 12 is a graph showing R_(free) (black line, solid squares),R_(work), (gray line, solid triangles), and R_(free)−R_(work) (dottedline, open circles) calculated at 2.9 Å for paired refinements in whichthe model was first refined against either 2.9, 2.7, 2.5, or 2.3 Å data.The chosen resolution cutoff of 2.3 Å (shaded) shows a decrease inR_(free) and increase in R_(work), which indicates that using the extraresolution improves the model.

FIGS. 13A and 13B show the 2.6 Å structure of AimA displays two calycindomains (FIG. 13A) and the amino terminal domain of AimA is connected bya short linker to the carboxy terminal domain and that both domainscontain an eight-stranded full (C-term) or partial (N-term) β-barrel(FIG. 13B).

FIGS. 14A-14D are a series of panels showing Structural homology of thetwo domains of AimA to avidins. FIG. 14A is a structural overlay ofN-term domain of AimA with top structural homology hit from PDBeFoldsearch, Streptomyces avindinii streptavidin (1swg). FIG. 14B is astructural overlay of C-term domain of AimA with top structural homologyhit from PDBeFold search, Danio rerio zebavidin (4bj8). FIG. 14C is aschematic of the biotin binding colorimetric assay. Biotin has higheraffinity for avidins than HABA does, so it replaces HABA in the bindingsite, thereby decreasing the absorbance at 500 nm. FIG. 14D is a graphshowing results from the biotin binding colorimetric assay. Biotinreplaces HABA binding in avidin, corresponding to a decrease inabsorbance when biotin is present. With AimA, there is no difference inabsorbance with or without biotin, indicating no biotin binding.

FIGS. 15A-15C are a series of panels showing the effect of AimA onintestinal inflammation in zebrafish. FIG. 15A is a graph showing thatfeeding zebrafish soy saponin induced increased intestinal neutrophilresponse, and treating those fish with 100 ng/ml purified AimA preventedthe increased intestinal neutrophil response. Letters indicatesignificantly different groups; ANOVA with multiple comparisons. Eachdot represents one fish; data collected from at least two independentexperiments; n≥24. FIG. 15B is a schematic showing a structural overlayof mouse lipocalin (PDB ID 3s26) and AimA C-term domain using PDBeFold.The β-strands are labeled according to canonical lipocalin nomenclature.Qscore is a structural overlay quality score that takes into accountboth the root mean standard deviation (RMSD) of the C_(α) carbons andthe alignment length. Qscore of 1 is perfect alignment, 0 is noalignment. The residues highlighted in orange are conserved in both thesequences and the structures. Displayed are the sequences ofStructurally Conserved Regions (SCR) 1 and 3 of a representative set ofkernel and outlier lipocalins (PDB accession numbers are shown inparentheses). The C-term domain of AimA is included and contains asubset of conserved SCR residues. Mouse lipocalin, SEQ ID NO: 23; mousemajor urinary protein, SEQ ID NO: 24; bovine BosD2, SEQ ID NO: 25;insect nitrophorin, SEQ ID NO: 26; AimA carboxy terminal domain, SEQ IDNO: 27; insect bilin binding protein, SEQ ID NO: 28; E. coli lipocalin,SEQ ID NO: 29; Motif, SEQ ID NO: 30. Bold residues are conserved acrossthe sequences. FIG. 15C is a graph showing treatment of conventionallyraised (CV) fish with soysaponin and lipocalin prevented AimA fromreducing the neutrophil response. Each dot represents one fish; n≥20from at least three independent experiments. Letters indicatesignificantly different groups; ANOVA with multiple comparisons.

FIGS. 16A-16C are a series of panels showing function of AimA domains.FIG. 16A is a schematic showing an overlay of C-term and N-term domainsof AimA using PDBeFold. FIG. 16B is a graph showing neutrophils inconventionally raised (CV) fish fed soysaponin (SS) and treated witheither purified full-length AimA or purified N-term (NT) or C-term (CT).Each dot represents the average percent of neutrophil influx in a flaskof 15 fish from the average neutrophil influx of a control flask(soysaponin only) of 15 fish. n≥9 flasks from at least three independentexperiments. Letters indicate significantly different groups; ANOVA withmultiple comparisons. FIG. 16C shows an overlay of C- and N-term domainsof AimA and mLCN using PDBeFold.

FIGS. 17A-17C are a series of panels showing structural comparison ofN-term and C-term domains of AimA. FIG. 17A is a structure-basedsequence alignment of N-term (amino acids 22-185 of SEQ ID NO: 1) andC-term (amino acids 192-313 of SEQ ID NO: 1) domains of AimA. Underlinedtext in C-term domain (and corresponding sequence in N-term domain)indicates regions that align in the structures. Arrows, β-strands, andcylinders, α-helices, above the text represent the secondary structure,with the top symbols corresponding to the N-term domain. Stars show theseven residues that align in the structures, with underlined starsindicating the Val and Thr residues that may be functionally relevant.FIG. 17B shows an overlay of N-term (orange) and C-term (teal) domain ofAimA. The seven structurally conserved residues are mapped. FIG. 17Cshows the full length AimA structure with the seven structurallyconserved regions shown as sticks.

FIGS. 18A and 18B are panels showing homologs to AimA across theAeromonas genus. FIG. 18A is a Clustal Omega alignment of six AimAhomologs with AimA. The predicted secretion signal, the linker betweenthe N- and C-term, and two possible lipocalin SCRs are indicated on thealignment. A. allosaccharophila, SEQ ID NO: 12; Aer AimA, SEQ ID NO: 1;A. hydrophila, SEQ ID NO: 13; A. salmonicida, SEQ ID NO: 14; A.schubertii, SEQ ID NO: 15; Aer AimB, SEQ ID NO: 11; A sobria, SEQ ID NO:16. FIG. 18B is a graph showing in vitro growth curves of Aer ΔaimA, AerΔaimB, and Aer ΔAΔB in A. veronii strain Hm21 (top), and ZF Aer ΔaimA inthe zebrafish Aeromonas background (bottom) do not have growth defectsin vitro.

FIGS. 19A-19E are a series of panels showing that AimA reducesneutrophil influx and promotes colonization of Aeromonas. FIG. 19A showsa structural overlay of AimA and the model of AimB (gray) generated byI-TASSER using AimA as a threading structure. FIG. 19B is a graphshowing intestinal neutrophil response to wild-type Aeromonas, ΔAimA,ΔAimB, and ΔAΔB. Each of the single mutants induces a similar neutrophilresponse to wild type, while the double mutant induces significantlygreater response. This phenotype is rescued by treatment with 100 ng/mlpurified AimA. FIG. 19C is a graph showing colonization level ofwild-type Aeromonas, ΔAimA, ΔAimB, and ΔAΔB. Each of the single mutantscolonized as well as wild type, while the double mutant had asignificantly reduced colonization level. This phenotype was rescued bytreatment with 100 ng/ml purified AimA. Neutrophil response wasincreased (FIG. 19D) and colonization level was decreased FIG. 19E inthe zebrafish Aeromonas isolate AimA deletion. For all graphs, each dotrepresents one fish; n≥23 from at least three independent experiments.Letters indicate significantly different groups, ANOVA with multiplecomparisons.

FIGS. 20A-20E are a series of panels showing that increased neutrophilresponse to Aeromonas ΔAΔB causes decreased survival rate. FIG. 20A is agraph showing the per capita effect of wild-type Aeromonas, ΔAimA,ΔAimB, and ΔAΔB. Each dot represents the average neutrophil responsefrom a flask of 15 fish divided by the average colonization level from aflask of 15 fish, normalized to 10⁴. FIG. 20B is a graph showingsurvival curves of zebrafish mono-associated with each of the A. veroniistrain Hm21 Aim mutants. Colonization with any of the Aim proteinmutants reduced host survival by three days post-infection. *indicatessignificant difference from the survival curve with wild-type Aeromonas,Mantel-Cox test. FIG. 20C is a graph showing that myd88^(−/−) transgenicfish lack a neutrophil response to bacteria. Each dot represents onefish. FIG. 20D is a graph showing survival curves of myd88^(−/−)zebrafish over a 3-day infection. myd88^(−/−) mutants inoculated witheither wild-type or ΔAΔB Aeromonas experienced a reduction in survivalby 3-days post infection. FIG. 20E is a graph showing ΔAΔB colonizationwas rescued to wild-type colonization levels in myd88^(−/−) transgenicfish. Further, both wild-type Aeromonas and ΔAΔB reached significantlyhigher colonization levels in the myd88^(−/−) transgenic fish comparedto wild-type fish, indicating that the innate immune response limitscommensal bacterial growth. FIG. 20F is a graph showing survival curvesof conventionally raised (CV) fish treated with LPS or with LPS andAimA. *indicates significant difference from the survival curve with LPStreatment, Mantel-Cox test. For all graphs, letters indicatesignificance by ANOVA with multiple comparisons.

SEQUENCE LISTING

The nucleic and amino acid sequences provided herein or in theaccompanying Sequence Listing are shown using standard letterabbreviations for nucleotide bases and amino acids. Only one strand ofeach nucleic acid sequence is shown, but the complementary strand isunderstood as included by any reference to the displayed strand.

The Sequence Listing is submitted as an ASCII text file in the form ofthe file named Sequence_Listing.txt, which was created on Jan. 29, 2018,and is 33,282 bytes, which is incorporated by reference herein.

SEQ ID NO: 1 is an exemplary amino acid sequence of A. veronii AP (alsoreferred to as AimA or Aer AimA).

SEQ ID NO: 2 is an exemplary nucleic acid sequence encoding A. veroniiAP.

SEQ ID NOs: 3 and 4 are forward and reverse primers, respectively, foramplification of an A. veronii AP nucleic acid.

SEQ ID NOs: 5 and 6 are forward and reverse primers, respectively foramplification of a chloramphenicol resistance cassette.

SEQ ID NOs: 7-10 are primers used for amplification of an approximately1000 base pair region upstream and downstream of the AP gene in A.veronii Hm21.

SEQ ID NO: 11 is the amino acid sequence of A. veronii AimB protein.

SEQ ID NO: 12 is the amino acid sequence of an A. allosaccharophila AIMprotein.

SEQ ID NO: 13 is the amino acid sequence of an A. hydrophila AIMprotein.

SEQ ID NO: 14 is the amino acid sequence of an A. salmonicida AIMprotein.

SEQ ID NO: 15 is the amino acid sequence of an A. schubertii AIMprotein.

SEQ ID NO: 16 is the amino acid sequence of an A. sobria AIM protein.

SEQ ID NO: 17 is a nucleic acid sequence encoding A. veronii AimB.

SEQ ID NO: 18 is a nucleic acid sequence encoding an A.allosaccharophila AIM protein.

SEQ ID NO: 19 is a nucleic acid sequence encoding an A. hydrophila AIMprotein.

SEQ ID NO: 20 is a nucleic acid sequence encoding an A. salmonicida AIMprotein.

SEQ ID NO: 21 is a nucleic acid sequence encoding an A. schubertii AIMprotein.

SEQ ID NO: 22 is a nucleic acid sequence encoding an A. sobria AIMprotein.

SEQ ID NO: 23 is SCR 1 and SCR3 amino acid sequences from mouselipocalin.

SEQ ID NO: 24 is SCR 1 and SCR3 amino acid sequences from mouse majorurinary protein.

SEQ ID NO: 25 is SCR 1 and SCR3 amino acid sequences from bovine BosD2.

SEQ ID NO: 26 is SCR 1 and SCR3 amino acid sequences from insectnitrophorin.

SEQ ID NO: 27 is SCR 1 and SCR3 amino acid sequences from AimA carboxyterminal domain.

SEQ ID NO: 28 is SCR 1 and SCR3 amino acid sequences from insect bilinbinding protein.

SEQ ID NO: 29 is SCR 1 and SCR3 amino acid sequences from E. colilipocalin.

SEQ ID NO: 30 is SCR 1 and SCR3 “motif” amino acid sequences.

DETAILED DESCRIPTION I. Abbreviations

AIM Aeromonas immune modulator (also referred to as AP or protein 1882,in some cases)

AP bacterial anti-inflammatory protein (also referred to as protein1882)

BTD beta-trefoil domain

CFS cell-free supernatant

CV conventionally reared

DPF days post-fertilization

DT2SS or ΔT2SS type II secretion system deletion

GF germ-free reared

GFP green fluorescent protein

IBD inflammatory bowel disease

MPO myeloperoxidase

T2SS type II secretion system

WT wild type

II. Terms

Unless otherwise noted, technical terms are used according toconventional usage. Unless otherwise explained, all technical andscientific terms used herein have the same meaning as commonlyunderstood by one of ordinary skill in the art to which this disclosurebelongs. The singular terms “a,” “an,” and “the” include pluralreferents unless context clearly indicates otherwise. Although methodsand materials similar or equivalent to those described herein can beused in the practice or testing of the present disclosure, suitablemethods and materials are described below.

All publications, patent applications, patents, public database entries(e.g., nucleic acid or amino acid Accession Nos.) and other referencesmentioned herein are incorporated by reference in their entirety. Incase of conflict, the present specification, including explanations ofterms, will control. In addition, the materials, methods, and examplesare illustrative only and not intended to be limiting.

In order to facilitate review of the various embodiments of thedisclosure, the following explanations of specific terms are provided:

Effective amount: An amount of an agent or composition that alone, ortogether with a pharmaceutically acceptable carrier and/or one or moreadditional agents, induces the desired response. Effective amounts of anagent can be determined in many different ways, such as assaying for areduction in neutrophil recruitment, delay (or even prevention) of onsetof a condition associated with inflammation, or a reduction oramelioration of one or more symptoms of a subject with inflammation.Effective amounts also can be determined through various in vitro, invivo, or in situ assays, including, but not limited to those describedherein.

Germ-free: An animal born and reared in aseptic conditions having nomicroorganisms living on or in it (for example, no bacteria in the gutof the animal).

Gnotobiotic: An animal in which only known strains of microorganisms arepresent. For example, a germ-free animal exposed to (e.g., intentionallyinoculated with) one or more known bacterial strains is gnotobiotic.Germ-free animals are also gnotobiotic, as their microbial status isknown. In contrast, conventionally reared animals (born and raisedwithout absolute control of microorganism exposure) have a microbiota ofmany, and in most cases hundreds or thousands of organisms, whichpopulation will vary from animal to animal.

Gut: The term “gut” is used herein to refer to the digestive tract.Zebrafish do not have a stomach, rather their gut includes an intestinalbulb, the mid-intestine, and the caudal intestine (beginning at theesophageal junction and ending at the anus). The function of thezebrafish gut is analogous to the small and large intestine in mammals.Therefore, in some examples, gut refers to the intestine (such as thesmall and/or large intestine).

Isolated: An “isolated” or “purified” biological component (such as anucleic acid, peptide, protein, or cell) has been substantiallyseparated, produced apart from, or purified away from other biologicalcomponents in which the component naturally occurs, for example, otherchromosomal and extrachromosomal DNA and RNA, proteins, and/or cells.Nucleic acids, peptides and proteins that have been “isolated” or“purified” thus include nucleic acids and proteins purified by standardpurification methods. The term also embraces nucleic acids, peptides andproteins prepared by recombinant expression in a host cell, as well aschemically synthesized nucleic acids or proteins.

The term “isolated” or “purified” does not require absolute purity;rather, it is intended as a relative term. Thus, for example, anisolated biological component is one in which the biological componentis more enriched than the biological component is in its standardenvironment or a production vessel. Preferably, a preparation ispurified such that the biological component represents at least 50%,such as at least 70%, at least 90%, at least 95%, or greater, of thetotal biological component content of the preparation.

Heterologous: Originating from a different genetic sources or species.For example, a nucleic acid that is heterologous to a cell originatesfrom an organism or species other than the cell in which it isexpressed. In one specific, non-limiting example, a heterologous nucleicacid includes an Aeromonas veronii nucleic acid that is present orexpressed in a different bacterial cell (such as an E. coli cell) or inan algal, plant, or mammalian cell. Methods for introducing aheterologous nucleic acid into bacterial, algal, plant, and mammaliancells are well known in the art, for example transformation with anucleic acid, including electroporation, lipofection, and particle gunacceleration.

In another example of use of the term heterologous, a nucleic acidoperably linked to a heterologous promoter is from an organism orspecies other than that of the promoter. For example, an Aeromonasveronii acid may be linked to a heterologous bacterial, viral, ormammalian promoter. In other examples of the use of the termheterologous, a nucleic acid encoding a polypeptide (such as ananti-inflammatory polypeptide disclosed herein) or portion thereof isoperably linked to a heterologous nucleic acid encoding a secondpolypeptide or portion thereof, for example to form a non-naturallyoccurring fusion protein.

Inflammation: A localized protective response elicited by injury totissue that serves to sequester the inflammatory agent. Inflammation isorchestrated by a complex biological response of vascular tissues toharmful stimuli, such as pathogens, damaged cells, or irritants. It is aprotective attempt by the organism to remove the injurious stimuli aswell as initiate the healing process for the tissue. An inflammatoryresponse is characterized by an accumulation of white blood cells,either systemically or locally at the site of inflammation. Theinflammatory response may be measured by many methods well known in theart, such as the number of white blood cells, the number ofpolymorphonuclear leukocytes (PMN, such as neutrophils, eosinophils,basophils, and/or mast cells), a measure of the degree of PMNactivation, or a measure of the amount of cytokines present.

A primary inflammation disorder is a disorder that is caused by theinflammation itself. A secondary inflammation disorder is inflammationthat is the result of another disorder. Inflammation can lead toinflammatory diseases, such as rheumatoid arthritis, osteoarthritis,inflammatory lung disease (including chronic obstructive pulmonary lungdisease), inflammatory bowel disease (including ulcerative colitis andCrohn's Disease), Hirschsprung disease (such as Hirschsprung associatedenterocolitis), pelvic inflammatory disease, periodontal disease,polymyalgia rheumatica, atherosclerosis, systemic lupus erythematosus,systemic sclerosis, Sjogren's Syndrome, asthma, allergic rhinitis, andskin disorders (including dermatomyositis and psoriasis), irritablebowel syndrome, necrotizing enterocolitis, atopy, and the like.

Inflammation can be classified as either acute or chronic. Acuteinflammation is the initial response of the body to harmful stimuli andis achieved by the increased movement of plasma and leukocytes from theblood into the injured tissues. A cascade of biochemical eventspropagates and matures the inflammatory response, involving the localvascular system, the immune system, and various cells within the injuredtissue. Inflammation is typically self-limiting and resolution (forexample, clearance of activated inflammatory cells) occurs when thethreat of infection or tissue damage is eliminated. Prolongedinflammation, known as chronic inflammation, leads to a progressiveshift in the type of cells which are present at the site of inflammationand is characterized by simultaneous destruction and healing of thetissue from the inflammatory process.

Isolated: An “isolated” biological component (such as a nucleic acidmolecule, protein, or cell) has been substantially separated or purifiedaway from other biological components in the cell of the organism, orthe organism itself, in which the component naturally occurs, such asother chromosomal and extra-chromosomal DNA and RNA, proteins and/orcells. Nucleic acid molecules and proteins that have been “isolated”include nucleic acid molecules and proteins purified by standardpurification methods or prepared by recombinant expression in a hostcell, as well as chemically synthesized nucleic acid molecules andproteins.

Myeloperoxidase (MPO): An enzyme released by activated neutrophils thatmetabolizes hydrogen peroxide generated by the neutrophils and chlorideion to produce hypochlorous acid (HOCl), which is cytotoxic. MPOrequires heme as a cofactor.

Neutrophil: A type of white blood cell (also known as neutrophilgranulocytes) that is part of the class of polymorphonuclear leukocytes.They are the most abundant type of white blood cells in mammals. Duringacute inflammation, neutrophils are recruited to the site ofinflammation or injury by chemotaxis toward chemokines, complementfactors, leukotrienes, and/or fMLP. Neutrophils are phagocytic and caninternalize and kill many microorganisms. They also release variouscytotoxic compounds, including myeloperoxidase, defensins, cathepsin,alkaline phosphatase, lysozyme, NADPH oxidase, and gelatinase, throughthe process of degranulation.

Operably linked: A first nucleic acid is operably linked to a secondnucleic acid when the first nucleic acid is placed in a functionalrelationship with the second nucleic acid. For instance, a promoter isoperably linked to a coding sequence if the promoter affects thetranscription or expression of the coding sequence. Generally, operablylinked DNA sequences are contiguous and, where necessary to join twoprotein-coding regions, in the same reading frame.

Recombinant: A nucleic acid or protein that is not naturally occurringor has a sequence that is made by an artificial combination of twootherwise separated segments of nucleotides or amino acids. Thisartificial combination is often accomplished by chemical synthesis or,more commonly, by the artificial manipulation of isolated segments ofnucleic acids, e.g., by genetic engineering techniques such as thosedescribed in Sambrook et al. Molecular Cloning: A Laboratory Manual,3^(rd) ed., Cold Spring Harbor Laboratory Press, N Y, 2001. The termrecombinant includes nucleic acids or proteins that have been alteredsolely by addition, substitution, or deletion of a portion of thenucleic acid sequence or amino acid sequence, respectively.

Sample (or biological sample): A specimen containing genomic DNA, RNA(including mRNA), protein, or combinations thereof, obtained from asubject. Examples include, but are not limited to, peripheral blood (orfractions thereof), fine needle aspirate, urine, saliva, feces, tissuebiopsy, surgical specimen, and autopsy material. In one example, asample includes a tumor biopsy (such as a colorectal tumor tissuebiopsy) or an intestinal tissue biopsy.

Sequence identity/similarity: The identity/similarity between two ormore nucleic acid sequences, or two or more amino acid sequences, isexpressed in terms of the identity or similarity between the sequences.Sequence identity can be measured in terms of percentage identity; thehigher the percentage, the more identical the sequences are. Sequencesimilarity can be measured in terms of percentage similarity (whichtakes into account conservative amino acid substitutions); the higherthe percentage, the more similar the sequences are.

Methods of alignment of sequences for comparison are well known in theart. Various programs and alignment algorithms are described in: Smith &Waterman, Adv. Appl. Math. 2:482, 1981; Needleman & Wunsch, J. Mol.Biol. 48:443, 1970; Pearson & Lipman, Proc. Natl. Acad. Sci. USA85:2444, 1988; Higgins & Sharp, Gene, 73:237-44, 1988; Higgins & Sharp,CABIOS 5:151-3, 1989; Corpet et al., Nuc. Acids Res. 16:10881-90, 1988;Huang et al., Computer Appls. in the Biosciences 8, 155-65, 1992; andPearson et al., Meth. Mol. Bio. 24:307-31, 1994. Altschul et al., J.Mol. Biol. 215:403-10, 1990, presents a detailed consideration ofsequence alignment methods and homology calculations. The NCBI BasicLocal Alignment Search Tool (BLAST) (Altschul et al., J. Mol. Biol.215:403-10, 1990) is available from several sources, including theNational Center for Biotechnology (NCBI, National Library of Medicine,Building 38A, Room 8N805, Bethesda, Md. 20894) and on the Internet, foruse in connection with the sequence analysis programs blastp, blastn,blastx, tblastn and tblastx. Additional information can be found at theNCBI web site.

One of skill in the art will appreciate that the particular sequenceidentity ranges provided herein are for guidance only; it is possiblethat strongly significant homologs or orthologs could be obtained thatfall outside the ranges provided.

Subject: Living multi-cellular vertebrate organism, a category thatincludes vertebrates, including human and non-human mammals.

Therapeutically effective amount: An amount of an agent or compositionthat alone, or together with a pharmaceutically acceptable carrierand/or one or more additional therapeutic agents, induces the desiredresponse. Effective amounts of an agent can be determined in manydifferent ways, such as assaying for a reduction in inflammation, delay(or even prevention) of onset of a condition associated withinflammation (such as inflammatory bowel disease), or a reduction oramelioration of one or more symptoms of a subject with inflammation.Effective amounts also can be determined through various in vitro, invivo, or in situ assays.

Transduced and Transformed: A virus or vector “transduces” a cell whenit transfers nucleic acid into the cell. A cell is “transformed” by anucleic acid transduced into the cell when the DNA becomes replicated bythe cell, either by incorporation of the nucleic acid into the cellulargenome, or by episomal replication. As used herein, the termtransformation encompasses all techniques by which a nucleic acidmolecule might be introduced into such a cell, including transfectionwith viral vectors, transformation with plasmid vectors, andintroduction of naked DNA by electroporation, lipofection, or particlegun acceleration.

Treating or Inhibiting: “Inhibiting” refers to inhibiting or reducingthe full development of a condition or symptom (such as inflammation oran inflammatory response) or a disorder (such as an inflammatorydisease). Inhibition of a condition or disease can span the spectrumfrom partial inhibition (reduction) to substantially complete inhibition(prevention) of the condition, symptom, or disease. In some examples,the term “inhibiting” refers to reducing or delaying the onset orprogression of inflammation, an inflammatory response, or aninflammatory disease. In contrast, “treatment” refers to a therapeuticintervention that ameliorates a sign or symptom of a disease orpathological condition (such as an inflammatory disease) after it hasbegun to develop.

Vector: A nucleic acid molecule that can be introduced into a host cell,thereby producing a transformed or transduced host cell. Recombinant DNAvectors are vectors including recombinant DNA. A vector can includenucleic acid sequences that permit it to replicate in a host cell, suchas an origin of replication. A vector can also include one or moreselectable marker genes, a cloning site for introduction of heterologousnucleic acids, a promoter (for example for expression of an operablylinked nucleic acid), and/or other genetic elements known in the art.Vectors include plasmid vectors, including plasmids for expression ingram negative and gram positive bacterial cell. Exemplary vectorsinclude those for use in E. coli. Vectors also include viral vectors,such as, but not limited to, retrovirus, orthopox, avipox, fowlpox,capripox, suipox, adenovirus, herpes virus, alpha virus, baculovirus,Sindbis virus, vaccinia virus, and poliovirus vectors. Vectors alsoinclude vectors for expression in yeast cells.

In some examples, a heterologous nucleic acid (such as a nucleic acidencoding an A. veronii protein) is introduced into a vector to produce arecombinant vector, thereby allowing the nucleic acid to be renewablyproduced and or a protein encoded by the nucleic acid to be expressed.

III. Anti-Inflammatory Protein from Aeromonas

Disclosed herein are anti-inflammatory proteins from members of theintestinal microbiota, including Aeromonas veronii. In some embodiments,the anti-inflammatory protein is a polypeptide that comprises orconsists of the amino acid sequence as set forth as SEQ ID NO: 1. Inother embodiments, the anti-inflammatory protein is a polypeptide thatcomprises or consists of the amino acid sequence of SEQ ID NO: 11. Instill further embodiments, the anti-inflammatory protein is apolypeptide that comprises or consists of the amino acid sequence of anyone of SEQ ID NOs: 12-16.

In additional embodiments, an anti-inflammatory polypeptide disclosedherein has at least 75%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequenceidentity to the amino acid sequence set forth in any one of SEQ ID NOs:1 or 11-16. In other embodiments, the anti-inflammatory protein does notinclude the signal sequence, which is removed from the mature protein.In some examples, the signal sequence is predicted to include the first22 amino acids of SEQ ID NO: 1. Thus, in some examples, the maturepolypeptide can have an amino acid sequence with at least 80%, 85%, 90%,95%, 96%, 97%, 98%, 99%, or 100% sequence identity to amino acids 23-313of SEQ ID NO: 1. In other examples, the mature anti-inflammatory has anamino acid sequence with at least 80%, 85%, 90%, 95%, 96%, 97%, 98%,99%, or 100% sequence identity to any one of SEQ ID NOs: 11-16, butlacking the predicted secretion signal shown in FIG. 18A. In oneexample, the mature polypeptide has an amino acid sequence with at least80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity toamino acids 21-330 of SEQ ID NO: 11.

Exemplary sequences can be obtained using computer programs that arereadily available on the internet and the amino acid sequences set forthherein. In some examples, the polypeptide retains a function of theanti-inflammatory protein, such as decreasing the number or activationof neutrophils and/or reducing or inhibiting inflammation in a subject.

In additional embodiments, an anti-inflammatory protein (such as any oneof SEQ ID NOs: 1 and 11-16) includes a portion or fragment of theprotein. In some examples, the anti-inflammatory protein or portionthereof includes at least 20 contiguous amino acids of any one of SEQ IDNOs: 1 and 11-16, for example, at least 30, at least 50, at least 75, atleast 100, at least 150, at least 200, at least 250, at least 300, atleast 350, at least 400, at least 450, or more amino acids of theprotein. In one example, a fragment of AP includes the mature protein(for example, AP that does not include the signal sequence, such asamino acids 23-313 of SEQ ID NO: 1). In other examples, a portion orfragment of an anti-inflammatory protein includes one or more domains ofAP. In some examples, a domain may include a portion of AP withstructural similarity to a β-trefoil domain (for example, withsimilarity to a BTD found in one or more cytokines), such as amino acids103-176 of SEQ ID NO: 1 or amino acids 148-176 of SEQ ID NO: 1. One ofordinary skill in the art will recognize that the boundaries of thedomain are not exact and in some examples may include additional orfewer amino acids (for example, about 20, 19, 18, 17, 16, 15, 14, 13,12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 more or less amino acids fromeither end of the domain).

In other embodiments, the anti-inflammatory protein includes anN-terminal domain or a C-terminal domain of any one of SEQ ID NOs: 1 and11-16. In some embodiments, the N-terminal domain or the C-terminaldomain of any one of SEQ ID NOs: 1 and 11-16 is about 130-190 aminoacids in length (such as about 130-150, 1430-160, 150-170, or 170-190amino acids in length). In some examples, the anti-inflammatory proteinincludes or consists of the N-terminal domain of Aer AimA (such as aminoacids 1-185, or amino acids 23-185 of SEQ ID NO: 1). In other examples,the anti-inflammatory protein includes or consists of the C-terminaldomain of Aer Aim A (such as amino acids 192-313 of SEQ ID NO: 1). Instill other examples, the anti-inflammatory protein includes or consistsof the N-terminal domain of Aer AimB (such as amino acids 1-188, oramino acids 21-188 of SEQ ID NO: 11). In further examples, theanti-inflammatory protein includes or consists of the C-terminal domainof Aer AimB (such as amino acids 189-330 of SEQ ID NO: 11). Theboundaries of the N-terminal and C-terminal domains are not exact and insome examples may include additional or fewer amino acids (for example,about 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3,2, or 1 more or less amino acids from either end of the domain). Thus insome examples, an AimA or AimB (or corresponding protein from anotherspecies) N-terminal domain may include about the first 170-190 aminoacids of the protein and an AimA or AimB (or corresponding protein fromanother species) C-terminal domain may include from about amino acid 170to amino acid 190 to the end of the protein.

Furthermore, one of ordinary skill in the art can identify correspondinganti-inflammatory AP proteins and/or domains from otheranti-inflammatory AP proteins, for example a corresponding AP from abacterium other than A. veronii or from another organism. Exemplaryproteins related to the A. veronii AP protein (such as SEQ ID NO: 1)include proteins from Aeromonas salmonicida (e.g., GenBank Accession No.WP_034524138.1; SEQ ID NO: 14), Aeromonas sobria (e.g., GenBankAccession No. WP_042019195.1), Aeromonas bestiarum (e.g., GenBankAccession No. WP_043556138), Aeromonas piscicola (e.g., GenBankAccession No. WP_042869769.1), and Aeromonas jandaei (e.g., GenBankAccession No. WP_041209781.1).

Minor modifications of an anti-inflammatory protein primary amino acidsequence (such as the Aeromonas AP (AimA) or AimB disclosed herein) arealso disclosed herein. Such modifications may result in polypeptidesthat have substantially equivalent activity as compared to theunmodified counterpart polypeptide described herein. Such modificationsmay be deliberate, for example as by site-directed mutagenesis, or maybe spontaneous. All of the polypeptides produced by these modificationsare included herein. Thus, a specific, non-limiting example of ananti-inflammatory protein is a conservative variant of the protein (suchas a single conservative amino acid substitution, for example, one ormore conservative amino acid substitutions, for example 1-10conservative substitutions, 2-5 conservative substitutions, 4-9conservative substitutions, such as 1, 2, 5 or 10 conservativesubstitutions). In other examples, the protein may include one or morenon-conservative substitutions (for example 1-10 non-conservativesubstitutions, 2-5 non-conservative substitutions, 4-9 non-conservativesubstitutions, such as 1, 2, 5 or 10 non-conservative substitutions), solong as the protein retains anti-inflammatory activity.

In additional embodiments, the anti-inflammatory protein or portionthereof (such as an N-terminal domain or C-terminal domain) includes atag (such as an N-terminal or C-terminal tag), for example for use inprotein purification. One of skill in the art can select appropriatetags, such as a His-tag, a GST tag, or an antibody recognition sequence(such as a Myc-tag or HA-tag). The anti-inflammatory protein can also beproduced as a fusion protein, either to facilitate expression and/orpurification or to facilitate delivery to a subject. For example, fusionproteins including a therapeutic molecule (such as the disclosedanti-inflammatory proteins) and transferrin has been shown to be usefulfor oral delivery routes. In other examples, the disclosedanti-inflammatory proteins may include a detectable label, such as aradioisotope, fluorophore, or hapten.

Additional exemplary Aeromonas anti-inflammatory proteins include theamino acid sequences of GenBank Accession Nos. WP_021230730 (SEQ ID NO:1), WP_005340784, WP_005357002, YP_004390739, WP_005342535,YP_001142339, WP_021140301, and WP_005310485; all of which areincorporated herein by reference as present in GenBank on May 16, 2014.One of ordinary skill in the art can identify additional candidateanti-inflammatory proteins related to the anti-inflammatory proteinsdisclosed herein, for example from other microbiota (for example, otherbacteria from the zebrafish gut or bacteria from mammalian gut, such ashuman microbiota).

The structure of SEQ ID NO: 1 (also referred to herein as AP or protein1882 or Aer AimA) was analyzed for conserved features using HHpred(available on the World Wide Web at toolkit.tuebingen.mpg.de/hhpred)using the AP sequence and selecting all protein databases. As shown inFIG. 7A, the N-terminus showed similarity to secretion signal sequences,consistent with this protein being processed by the type II secretionsystem (discussed in Example 1). In addition, the protein showedsimilarity to decaheme cytochrome C of Shewanella oneidensis (aminoacids 6-175 of SEQ ID NO: 1) and to a beta-trefoil domain (BTD) that isalso found in cytokines, including interleukin-18 (IL-18), andinterleukin-1b (IL-1b). In some examples, the BTD domain includes aminoacids 103-176 of SEQ ID NO: 1 or amino acids 148-176 of SEQ ID NO: 1.

As discussed above, AP includes a region that is predicted to contain aβ-trefoil domain with homology to human cytokines IL-1β, IL-la, andIL-1ra. Both IL-1β and IL-la bind the type 1 IL-1 receptor (IL-1R1).IL-1R1 engages with the IL-1 receptor accessory protein (IL-1RAP) toform a complex that results in the recruitment of the MyD88 adaptorprotein (FIG. 7B). This initiates a signaling cascade that causes thetranscription factor, NF-κB, to translocate into the nucleus andinitiate transcription of the pro-inflammatory cytokines Il1β, Il6, Il8,and tnfα. Interleukin 1 receptor antagonist (IL-1ra) dampens IL-1signaling by binding IL-1R1 and preventing receptor complex formationwith IL-1RAP. Normal function and levels of IL-1ra affect ulcerativecolitis, and polymorphisms in the IL-1ra gene are associated withseverity and susceptibility to UC (Carter et al., Genes Immun. 5:8-15,2004), neutralizing IL-1ra exacerbates colitis (Feretti et al., J. Clin.Invest. 94:449-453, 1994), and administering exogenous IL-1ra (Ricci etal., BMC Biotechnol. 3:15, 2003) or inducing endogenous IL-1ra (Gresnigtet al., PLoS Pathog. 10:e1003936, 2014) reduces disease severity inanimal models of inflammation (Dinarello, Blood 89:2095-2147, 1996;Dinarello Blood 118:3720-3732, 2011). The IL-1 family of cytokines(Huising et al. Dev. Comp. Immunol. 28:395-413, 2004) and neutrophilbehavior and activity (Renshaw et al., Blood 108:3976-3978, 2006;Guyader et al. Blood 111:132-141, 2008) are conserved in zebrafish.Moreover, intestinal neutrophil influx in zebrafish depends on Myd88(Bates et al., Cell Host Microbe 2:371-382, 2007), confirming thispathway's role in neutrophil behavior. Without being bound by theory,based on the biological activity and homology of AP, it is believed thatAP may be a competitive inhibitor of binding sites on the cytokinereceptor IL-1R1, potentially decreasing pro-inflammatory IL-1 signaling.

In additional embodiments, the anti-inflammatory protein disclosedherein (referred to as AP or Aer AimA is encoded by a nucleic acidsequence which comprises or consists of the nucleic acid sequence setforth as SEQ ID NO: 2. In further embodiments, the anti-inflammatoryprotein disclosed herein is encoded by a nucleic acid sequence whichcomprises or consists of the nucleic acid sequence of any one of SEQ IDNOs: 17-22.

In additional embodiments, a nucleic acid encoding an Aeromonasanti-inflammatory polypeptide disclosed herein has at least 75%, 85%,90%, 95%, 96%, 97%, 98%, or 99% sequence identity to the nucleic acidsequence set forth in SEQ ID NO: 2 or a fragment thereof. In otherembodiments, a nucleic acid encoding an Aeromonas anti-inflammatorypolypeptide disclosed herein has at least 75%, 85%, 90%, 95%, 96%, 97%,98%, or 99% sequence identity to the nucleic acid sequence of any one ofSEQ ID NOs: 17-22 or a fragment thereof. For example, the nucleic acidcan have a nucleic acid sequence with at least 80%, 85%, 90%, 95%, 96%,97%, 98%, 99%, or 100% sequence identity to a nucleic acid encodingamino acids 23-313 of SEQ ID NO: 1 (such as nucleotides 67-939 of SEQ IDNO: 2) or a nucleic acid encoding amino acids 103-176 of SEQ ID NO: 1(such as nucleotides 307-528 of SEQ ID NO: 2). In other examples, thenucleic acid has a nucleic acid sequence with at least 80%, 85%, 90%,95%, 96%, 97%, 98%, 99%, or 100% sequence identity to a nucleic acidencoding amino acids 21-330 of SEQ ID NO: 11 (such as nucleotides 61-564of SEQ ID NO: 17).

In other embodiments, the nucleic acid encodes includes an N-terminaldomain or a C-terminal domain of any one of SEQ ID NOs: 2 and 17-22. Insome embodiments, the N-terminal or C-terminal domain is about 390-570nucleotides in length (such as about 390-450, 420-480, 450-510, 480-540,or 510-570 nucleotides in length). In some examples, the nucleic acidencodes an N-terminal domain of Aer AimA (for example, encodes aminoacids 1-185, or amino acids 23-185 of SEQ ID NO: 1, such as nucleotides1-555 or 67-555 of SEQ ID NO: 2). In other examples, the nucleic acidencodes a C-terminal domain of Aer Aim A (for example, encodes aminoacids 192-313 of SEQ ID NO: 1, such as nucleotides 574-939 of SEQ ID NO:2). In still other examples, the nucleic acid encodes an N-terminaldomain of Aer AimB (for example, encodes amino acids 1-188, or aminoacids 21-188 of SEQ ID NO: 11, for example, nucleic acids 1-564 or61-564 of SEQ ID NO: 17). In further examples, the nucleic acid encodesa C-terminal domain of Aer AimB (for example, encodes amino acids189-330 of SEQ ID NO: 11, such as nucleotides 565-990 of SEQ ID NO: 17).The boundaries of the N-terminal and C-terminal domains are not exactand in some examples may include additional or fewer nucleotides (forexample, about 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6,5, 4, 3, 2, or 1 more or less nucleotides from either end of thedomain).

Exemplary sequences can be obtained using computer programs that arereadily available on the internet and the amino acid sequences set forthherein. In some examples, the nucleic acid encodes a polypeptide thatretains a function of the anti-inflammatory protein, such as decreasingthe number or activation of neutrophils and/or reducing or inhibitinginflammation in a subject.

Additional exemplary Aeromonas nucleic acids encoding the disclosedproteins include the nucleic acid sequences of GenBank Accession Nos.NZ_ATFB01000030 (nucleotides 64518-65459; SEQ ID NO: 2), NZ_JH815583(nucleotides 116798-117739, complement), NZ_JH815589 (nucleotides391175-392116, complement), NC_015424 (nucleotides 103273-104214),NZ_JH823256 (nucleotides 1061308-1062153), NC_009348 (nucleotides2743728-2744681, complement), NZ_ARYZ01000054 (nucleotides 2343-3290),and NZ_AGVO01000002 (nucleotides 295610-297457); all of which areincorporated herein by reference as present in GenBank on May 16, 2014.One of ordinary skill in the art can identify additional candidatenucleic acids encoding anti-inflammatory proteins related to theanti-inflammatory proteins disclosed herein, for example from othermicrobiota.

Minor modifications of nucleic acids encoding an anti-inflammatoryprotein primary amino acid sequence (such as the Aeromonas AP disclosedherein) are also contemplated herein. Such modifications to the nucleicacid may result in polypeptides that have substantially equivalentactivity as compared to the unmodified counterpart polypeptide describedherein. Such modifications may be deliberate, for example as bysite-directed mutagenesis, or may be spontaneous. All of the nucleicacids produced by these modifications are included herein. Thus, aspecific, non-limiting example of modified nucleic acid encoding ananti-inflammatory protein is a nucleic acid encoding conservativevariant of the protein (such as a single conservative amino acidsubstitution, for example, one or more conservative amino acidsubstitutions, for example 1-10 conservative substitutions, 2-5conservative substitutions, 4-9 conservative substitutions, such as 1,2, 5 or 10 conservative substitutions). In other examples, the nucleicacid may encode a protein including one or more non-conservativesubstitutions (for example 1-10 non-conservative substitutions, 2-5non-conservative substitutions, 4-9 non-conservative substitutions, suchas 1, 2, 5 or 10 non-conservative substitutions), so long as the encodedprotein retains anti-inflammatory activity.

In additional embodiments, the nucleic acid encoding theanti-inflammatory protein further includes a nucleic acid sequenceencoding a tag (such as an N-terminal or C-terminal tag), for examplefor use in protein purification. One of skill in the art can selectnucleic acids encoding appropriate tags, such as a His-tag, a GST tag,or an antibody recognition sequence (such as a Myc-tag or HA-tag). Thenucleic acid may also encode a fusion, for example, a nucleic acidencoding a fusion protein including a disclosed anti-inflammatoryproteins and transferrin. In other examples, the disclosed nucleic acidsmay include a detectable label, such as a radioisotope, fluorophore, orhapten.

Nucleic acid molecules encoding an anti-inflammatory protein disclosedherein also include a recombinant DNA which is incorporated into avector, into an autonomously replicating plasmid or virus, or into thegenomic DNA of a prokaryote or eukaryote, or which exists as a separatemolecule (such as a cDNA) independent of other sequences. A nucleic acidencoding an anti-inflammatory polypeptide (such as a nucleic acidencoding an Aeromonas anti-inflammatory peptide, for example SEQ ID NOs:1, 11-16, or a fragment thereof) is in some examples operably linked toheterologous expression control sequences. An expression controlsequence operably linked to a coding sequence is ligated such thatexpression of the coding sequence is achieved under conditionscompatible with the expression control sequences. The expression controlsequences include, but are not limited to, appropriate promoters,enhancers, transcription terminators, a start codon (e.g., ATG) in frontof a protein-encoding nucleic acid, splicing signal for introns,maintenance of the correct reading frame of that gene to permit propertranslation of mRNA, and stop codons. The expression control sequence(s)in some examples are heterologous expression control sequence(s), forexample from an organism or species other than the protein-encodingnucleic acid. Thus, the protein-encoding nucleic acid operably linked toa heterologous expression control sequence (such as a promoter)comprises a nucleic acid that is not naturally occurring. In otherexamples, the nucleic acid is operably linked to a tag sequence (such as6×His, HA tag, or Myc tag) or another protein-coding sequence, such asglutathione S-transferase or maltose binding protein.

Vectors for cloning and replication of the disclosed nucleic acidmolecules include bacterial plasmids, such as bacterial cloning orexpression plasmids. Exemplary bacterial plasmids into which the nucleicacids can be cloned include E. coli plasmids, such as pBR322, pUCplasmids (such as pUC18 or pUC19), pBluescript, pACYC184, pCD1, pGEM®plasmids (such as pGEM®-3, pGEM®-4, pGEM-T® plasmids; Promega, Madison,Wis.), TA-cloning vectors, such as pCR® plasmids (for example, pCR® II,pCR® 2.1, or pCR® 4 plasmids; Life Technologies, Grand Island, N.Y.) orpcDNA plasmids (for example pcDNA™ 3.1 or pcDNA™ 3.3 plasmids; LifeTechnologies). In some examples, the vector includes a heterologouspromoter which allows protein expression in bacteria. Exemplary vectorsinclude pET vectors (for example, pET-21b), pDEST™ vectors (LifeTechnologies), pRSET vectors (Life Technologies), pBAD vectors, and pQEvectors (Qiagen). The disclosed nucleic acids can be also be cloned intoB. subtilis plasmids, for example, pTA1060 and pHT plasmids (such aspHT01, pHT43, or pHT315 plasmids). One of skill in the art can selectadditional vectors suitable for cloning and/or bacterial expression ofanti-inflammatory proteins such as those disclosed herein.

In other embodiments, vectors are used for expression in yeast such asS. cerevisiae or Kluyveromyces lactis. Several promoters are known to beof use in yeast expression systems such as the constitutive promotersplasma membrane H⁺-ATPase (PMA1), glyceraldehyde-3-phosphatedehydrogenase (GPD), phosphoglycerate kinase-1 (PGK1), alcoholdehydrogenase-1 (ADH1), and pleiotropic drug-resistant pump (PDR5). Inaddition, many inducible promoters are of use, such as GAL1-10 (inducedby galactose), PHO5 (induced by low extracellular inorganic phosphate),and tandem heat shock HSE elements (induced by temperature elevation to37° C.). Promoters that direct variable expression in response to atitratable inducer include the methionine-responsive MET3 and MET25promoters and copper-dependent CUP1 promoters. Any of these promotersmay be cloned into multicopy (20 or single copy (CEN) plasmids to givean additional level of control in expression level. The plasmids caninclude nutritional markers (such as URA3, ADE3, HIS1, and others) forselection in yeast and antibiotic resistance (such as AMP) forpropagation in bacteria. Plasmids for expression on K. lactis are known,such as pKLAC1. Thus, in one example, after amplification in bacteria,plasmids can be introduced into the corresponding yeast auxotrophs bymethods similar to bacterial transformation.

Viral vectors including the disclosed polynucleotides (such aspolynucleotides encoding an anti-inflammatory protein) can also beprepared. A number of viral vectors have been constructed, includingpolyoma, SV40 (Madzak et al., 1992, J. Gen. Virol., 73:15331536),adenovirus (Berkner, 1992, Curr. Top. Microbiol. Immunol., 158:39-6;Berliner et al., 1988, BioTechniques, 6:616-629; Gorziglia et al., 1992,J. Virol., 66:4407-4412; Quantin et al., 1992, Proc. Natl. Acad. Sci.USA, 89:2581-2584; Rosenfeld et al., 1992, Cell, 68:143-155; Wilkinsonet al., 1992, Nucl. Acids Res., 20:2233-2239; Stratford-Perricaudet etal., 1990, Hum. Gene Ther., 1:241-256), vaccinia virus (Mackett et al.,1992, Biotechnology, 24:495-499), adeno-associated virus (Muzyczka,1992, Curr. Top. Microbiol. Immunol. 158:91-123; On et al., 1990, Gene,89:279-282), herpes viruses including HSV and EBV (Margolskee, 1992,Curr. Top. Microbiol. Immunol., 158:67-90; Johnson et al., 1992, J.Virol., 66:2952-2965; Fink et al., 1992, Hum. Gene Ther. 3:11-19;Breakfield et al., 1987, Mol. Neurobiol., 1:337-371; Fresse et al.,1990, Biochem. Pharmacol., 40:2189-2199), Sindbis viruses (Herweijer etal., 1995, Hum. Gene Ther. 6:1161-1167; U.S. Pat. Nos. 5,091,309 and5,2217,879), alphaviruses (S. Schlesinger, 1993, Trends Biotechnol.11:18-22; Frolov et al., 1996, Proc. Natl. Acad. Sci. USA93:11371-11377) and retroviruses of avian (Brandyopadhyay et al., 1984,Mol. Cell Biol., 4:749-754; Petropouplos et al., 1992, J. Virol.,66:3391-3397), murine (Miller, 1992, Curr. Top. Microbiol. Immunol.,158:1-24; Miller et al., 1985, Mol. Cell Biol., 5:431-437; Sorge et al.,1984, Mol. Cell Biol., 4:1730-1737; Mann et al., 1985, J. Virol.,54:401-407), and human origin (Page et al., 1990, J. Virol.,64:5370-5276; Buchschalcher et al., 1992, J. Virol., 66:2731-2739).Baculovirus (Autographa californica multinuclear polyhedrosis virus;AcMNPV) vectors are also known in the art, and may be obtained fromcommercial sources (such as PharMingen, San Diego, Calif.; ProteinSciences Corp., Meriden, Conn.; Stratagene, La Jolla, Calif.).

DNA sequences encoding an anti-inflammatory polypeptide can be expressedin vitro by DNA transfer into a suitable host cell. The cell may beprokaryotic or eukaryotic. The term also includes any progeny of thesubject host cell. It is understood that all progeny may not beidentical to the parental cell since there may be mutations that occurduring replication. Methods of stable transfer, meaning that the foreignDNA is continuously maintained in the host, are known in the art.

Host cells can include microbial, yeast, insect and/or mammalian hostcells. Methods of expressing DNA sequences having eukaryotic or viralsequences in prokaryotes are well known in the art. Non-limitingexamples of suitable host cells include bacteria, archea, insect, fungi(for example, yeast), mycobacterium (such as M. smegmatis), plant, andanimal cells (for example, mammalian cells, such as human cells).Exemplary cells of use include E. coli, Bacillus subtilis, Saccharomycescerevisiae, Salmonella typhimurium, SF9 cells, C129 cells, 293 cells,Neurospora, and immortalized mammalian myeloid and lymphoid cell lines.Techniques for the propagation of mammalian cells in culture arewell-known (see, Jakoby and Pastan (eds), 1979, Cell Culture. Meth.Enzymol. volume 58, Academic Press, Inc., Harcourt Brace Jovanovich,N.Y.). Examples of commonly used mammalian host cell lines are VERO andHeLa cells, CHO cells, and WI38, BHK, and COS cell lines, although othercell lines may be used, such as cells designed to provide higherexpression, desirable glycosylation patterns, or other features. Asdiscussed above, techniques for the transformation of yeast cells, suchas polyethylene glycol transformation, protoplast transformation andgene guns are also known in the art (see Gietz and Woods Meth. Enzymol.350: 87-96, 2002).

Transformation of a host cell with recombinant DNA can be carried out byconventional techniques as are well known to those skilled in the art.Where the host is prokaryotic, such as, but not limited to, E. coli,competent cells which are capable of DNA uptake can be prepared fromcells harvested after exponential growth phase and subsequently treatedby the CaCl₂ method using procedures well known in the art.Alternatively, MgCl₂ or RbCl can be used. Transformation can also beperformed after forming a protoplast of the host cell if desired, or byelectroporation.

When the host is a eukaryote, such methods of transfection of DNA ascalcium phosphate coprecipitates, conventional mechanical proceduressuch as microinjection, electroporation, insertion of a plasmid encasedin liposomes, or virus vectors can be used. Eukaryotic cells can also beco-transformed with a polynucleotide encoding an anti-inflammatoryprotein polypeptide and a second foreign DNA molecule encoding aselectable phenotype, such as the herpes simplex thymidine kinase gene.Another method is to use a eukaryotic viral vector, such as simian virus40 (SV40) or bovine papilloma virus, to transiently infect or transformeukaryotic cells and express the protein (see for example, EukaryoticViral Vectors, Cold Spring Harbor Laboratory, Gluzman ed., 1982).

IV. Methods of Treating or Inhibiting Inflammation

Disclosed herein are methods of treating or inhibiting inflammation in asubject. In some embodiments, the methods include administering to asubject an effective amount of a microbial anti-inflammatory protein(such as an Aeromonas anti-inflammatory protein), including, but notlimited to the anti-inflammatory proteins disclosed herein (such as SEQID NOs: 1, 11-16, or fragments or portions thereof). Theanti-inflammatory protein may be administered in any form, includingadministration of cells producing an anti-inflammatory protein disclosedherein (e.g., A. veronii, A. salmonicida, or A. hydrophila, or otherbacteria recombinantly expressing or overexpressing an anti-inflammatoryprotein), a cell extract, or a preparation (such as a cell-freesupernatant) from a cell producing an anti-inflammatory protein, anisolated or purified anti-inflammatory protein (including, but notlimited to SEQ ID NO: 1, 11-16, or a fragment thereof), or a nucleicacid encoding an anti-inflammatory protein (including, but not limitedto, SEQ ID NO: 2, 17-22, or a portion thereof).

The anti-inflammatory proteins disclosed herein can be chemicallysynthesized by standard methods, or can be produced recombinantly. Anexemplary process for polypeptide production is described in Lu et al.,FEBS Lett. 429:31-35, 1998. They can also be isolated by methodsincluding preparative chromatography and immunological separations.Polypeptides can also be produced using molecular genetic techniques,such as by inserting a nucleic acid encoding an anti-inflammatoryprotein or a portion thereof into an expression vector, introducing theexpression vector into a host cell (such as E. coli), and isolating thepolypeptide (for example, as discussed in Section III). In someexamples, the protein includes a tag (such as an N-terminal orC-terminal tag), for example for use in protein purification. One ofskill in the art can select appropriate tags, such as a His-tag, a GSTtag, or an antibody recognition sequence (such as a Myc-tag or HA-tag).In some embodiments, the anti-inflammatory protein is produced bybacteria (such as Aeromonas or another suitable bacteria) expressing theanti-inflammatory protein from an expression vector (such as a vectorincluding a constitutive or a regulatable promoter). Theanti-inflammatory protein may be administered to a subject as anisolated preparation from the bacteria, an extract or other preparation(such as cell-free supernatant), or the recombinant bacteria may beadministered to the subject.

In some embodiments, the anti-inflammatory protein (such as a proteincomprising the sequence of SEQ ID NO: 1 or a protein that is at least80%, 85%, 90%, 95%, 98%, or 99% identical to SEQ ID NO: 1 or a fragmentthereof) or a nucleic acid encoding the protein or fragment thereof isadministered to a subject to treat or inhibit inflammation. In someexamples, a fragment of the anti-inflammatory protein includes theprocessed mature protein, for example, lacking the signal sequence (suchas amino acids 23-313 of SEQ ID NO: 1) or a domain of the protein (suchas a BTD domain, for example amino acids 103-176 of SEQ ID NO: 1 oramino acids 148-176 of SEQ ID NO: 1), or polypeptides that are at least80%, 85%, 90%, 95%, 98%, or 99% identical to the fragment of theanti-inflammatory protein. In other examples, a fragment of theanti-inflammatory protein includes an N-terminal or C-terminal domain(or both) of SEQ ID NO: 1, such as amino acids 1-185, or amino acids23-185 of SEQ ID NO: 1, and/or amino acids 192-313 of SEQ ID NO: 1.

In other embodiments, an anti-inflammatory protein (such as a proteinincluding the sequence of any one of SEQ ID NOs: 11-16, or a proteinthat is at least 80%, 85%, 90%, 95%, 98%, or 99% identical to any one ofSEQ ID NOs: 11-16 or a fragment thereof) or a nucleic acid encoding theprotein or fragment thereof is administered to a subject to treat orinhibit inflammation. In some examples, a fragment of theanti-inflammatory protein includes an N-terminal or C-terminal domain(or both) of SEQ ID NO: 11, such as amino acids 1-188, or amino acids21-188 of SEQ ID NO: 11, and/or amino acids 189-330 of SEQ ID NO: 11.

In some examples, administration of the anti-inflammatory protein orfragment thereof (or nucleic acid encoding the protein or fragmentthereof) reduces at least one marker of inflammation (such as number oractivation of neutrophils) by at least about 10% (such as at least 15%,at least 20%, at least 25%, at least 30%, at least 40%, at least 50%, atleast 60%, at least 70%, at least 80%, at least 90%, or more).

In some examples, the subject may have one of a number of conditionsbroadly categorized as an inflammatory disease or disorder. Suchdisorders include, but are not limited to, rheumatoid arthritis,osteoarthritis, inflammatory lung disease (including chronic obstructivepulmonary lung disease), inflammatory bowel disease (includingulcerative colitis and Crohn's Disease), Hirschsprung disease (such asHirschsprung's associated enterocolitis), pelvic inflammatory disease,periodontal disease, polymyalgia rheumatica, atherosclerosis, systemiclupus erythematosus, systemic sclerosis, Sjogren's Syndrome, asthma,allergic rhinitis, and skin disorders (including dermatomyositis andpsoriasis), irritable bowel syndrome, necrotizing enterocolitis, oratopy. In particular embodiments, the subject has inflammatory boweldisease.

In other examples, the subject may have or be suspected to have sepsisor septic shock. Sepsis is a condition where the subject has aninfection, and the subject's immune response to the infection damagesthe subject's own tissue(s). Sepsis is sometimes defined as presence ofinfection with systemic inflammatory response syndrome (SIRS). Sepsis istypically diagnosed by presence of infection in combination with alteredmental state, increased respiratory rate (e.g., >22 breaths/minute), andlow blood pressure (e.g., <100 mm Hg systolic pressure). Septic shock islow blood pressure due to sepsis that does not improve after treatment.Sepsis and septic shock are a life-threatening condition that is usuallytreated with antibiotics, intravenous fluids, and other supportivemeasures, such as oxygen, mechanical ventilation and/or dialysis. Animalmodels of sepsis include administration of lipopolysaccharide (LPS) toan animal (such as mice or zebrafish) and administration of intravenousbacteria (such as E. coli) in primate models, or cecal ligation andpuncture (CLP).

The anti-inflammatory protein, nucleic acid encoding theanti-inflammatory protein, or cell expressing the anti-inflammatoryprotein can be administered to a subject in need of treatment using anysuitable means known in the art. Methods of administration include, butare not limited to, intradermal, intramuscular, intraperitoneal,parenteral, subcutaneous, rectal, intranasal, inhalation, oral, or bygene gun. Intranasal administration refers to delivery of thecompositions into the nose and nasal passages through one or both of thenares and can include delivery by a spraying mechanism or dropletmechanism, or through aerosolization of the therapeutic agent. Inparticular examples, the anti-inflammatory protein, nucleic acidencoding the anti-inflammatory protein, or a preparation including theanti-inflammatory protein (such as a cell extract or preparation orcells expressing the protein) is administered orally. In furtherexamples, the anti-inflammatory protein, nucleic acid encoding theanti-inflammatory protein, or a preparation encoding theanti-inflammatory protein (such as a cell extract or preparation orcells expressing the protein) is administered intravenously. In otherexamples, the anti-inflammatory protein, nucleic acid encoding theanti-inflammatory protein, or a preparation encoding theanti-inflammatory protein (such as a cell extract or preparation orcells expressing the protein) is administered subcutaneously orintramuscularly.

Therapeutic agents can be administered in any suitable manner,preferably with pharmaceutically acceptable carriers. Pharmaceuticallyacceptable carriers are determined in part by the particular compositionbeing administered, as well as by the particular method used toadminister the composition. Accordingly, there is a wide variety ofsuitable formulations of pharmaceutical compositions of the presentdisclosure. The pharmaceutically acceptable carriers (vehicles) usefulin this disclosure are conventional. Remington: The Science and Practiceof Pharmacy, The University of the Sciences in Philadelphia, Editor,Lippincott, Williams, & Wilkins, Philadelphia, Pa., 21^(st) Edition(2005), describes compositions and formulations suitable forpharmaceutical delivery of one or more therapeutic agents

Preparations for parenteral administration include sterile aqueous ornon-aqueous solutions, suspensions, and emulsions. Examples ofnon-aqueous solvents are propylene glycol, polyethylene glycol,vegetable oils such as olive oil, and injectable organic esters such asethyl oleate. Aqueous carriers include water, alcoholic/aqueoussolutions, emulsions or suspensions, including saline and bufferedmedia. Parenteral vehicles include sodium chloride solution, Ringer'sdextrose, dextrose and sodium chloride, lactated Ringer's, or fixedoils. Intravenous vehicles include fluid and nutrient replenishers,electrolyte replenishers (such as those based on Ringer's dextrose), andthe like. Preservatives and other additives may also be present such as,for example, antimicrobials, anti-oxidants, chelating agents, and inertgases and the like.

Compositions for oral administration include powders or granules,suspensions or solutions in water or non-aqueous media, capsules,sachets, or tablets. Thickeners, flavorings, diluents, emulsifiers,dispersing aids or binders may be desirable.

The amount of anti-inflammatory protein, nucleic acid encoding theanti-inflammatory protein, or a preparation encoding theanti-inflammatory protein (such as a cell extract or preparation orcells expressing the protein) to be administered to a subject can beselected by one of ordinary skill in the art, for example from about 1μg to 5 g anti-inflammatory protein (such as about 10 μg to 1 g, 100 mto 500 mg, or 1 mg to 100 mg). In other examples, the amount ofanti-inflammatory protein or a preparation encoding theanti-inflammatory protein (such as a cell extract or preparation orcells expressing the protein) to be administered to a subject is about0.001 mg/kg to about 1000 mg/kg (such as about 0.01 mg/kg to about 500mg/kg, about 1 mg/kg to about 250 mg/kg, or about 10 mg/kg to 100mg/kg).

The dosage can be administered one or more times per day, in divideddoses (such as 2, 3, or 4 divided doses per day), or in a single dosagedaily. The dosage can also be administered every 2 days, every 3 days,bi-weekly, once weekly, semi-weekly, or monthly. In some examples, aneffective amount of anti-inflammatory protein is an amount that inhibitsor ameliorates one or more symptoms of an inflammatory disease. In otherexamples, an effective amount of anti-inflammatory protein is an amountthat decreases one or more markers of inflammation, such as number ofwhite blood cells (such as neutrophils).

In particular examples, prior to, during, or following administration ofa disclosed anti-inflammatory protein (or nucleic acid encoding theprotein, or preparation of bacteria expressing the protein) the subjectcan receive one or more other anti-inflammatory therapies. Examples ofsuch therapies include, but are not limited to, non-steroidalanti-inflammatory drugs (NSAIDs, such as aspirin, ibuprofen, naproxen,and celecoxib), corticosteroids (such as prednisone, methylprednisolone,or cortisone), or DMARDs (such as etanercept, adalimumab, infliximab,rituximab, or methotrexate). Combinations of these therapies can also beadministered to a subject. In other examples, such as when the subjecthas or is suspected to have sepsis or septic shock, one or more othertherapies, such as antibiotic therapy, intravenous fluids,vassopressors, or other supportive therapies, can be administered priorto, during, or following administration of a disclosed anti-inflammatoryprotein (or nucleic acid encoding the protein, or preparation ofbacteria expressing the protein).

V. Methods of Identifying Modulators of Inflammation

Disclosed herein are methods for identifying modulators of immuneresponses, such as inflammation. In some embodiments, the methodsinclude inoculating germ-free zebrafish (or a population of germ-freezebrafish) with one or more defined bacterial strains or CFS supernatantfrom one or more defined bacterial strains and/or one or more testcompounds and determining the amount of inflammation, for example bymeasuring a marker of inflammation. In some examples, the zebrafish aretransgenic for one or more genes, for example, are transgenic for greenfluorescent protein (GFP) expressed under the control of themyeloperoxidase (MPO) promoter. In other embodiments, the methodsinclude inoculating conventionally raised zebrafish (or a population ofconventionally raised zebrafish) with one or more test compounds anddetermining the amount of inflammation, for example by measuring amarker of inflammation. In some examples, the conventionally raisedzebrafish are transgenic or mutant for one or more genes, for example,Sox10.

In some examples, a marker of inflammation is the amount (such as numberor percentage) of neutrophils or macrophages present, for example in thegut of the zebrafish. Presence or amount of neutrophils or macrophagesin the gut can be determined by histological staining, in situhybridization, or immunohistochemistry. In one example, presence oramount of neutrophils is determined by detection of a marker expressedunder the control of a neutrophil-specific gene (such as greenfluorescent protein (GFP) expressed from the myeloperoxidase (MPO)promoter, as described below). In other examples, a marker ofinflammation is expression (such as the amount of expression) of one ormore inflammatory genes, for example cytokines (such as TNFα) orexpression of MPO. Expression of markers of inflammation can be detectedusing methods such as PCR (for example, RT-PCR, real-time PCR,quantitative real-time RT-PCR), in situ hybridization, Northernblotting, immunohistochemistry, Western blotting, flow cytometry,microscopy, or other techniques known to one of skill in the art.

In some examples, the presence or amount of the marker of inflammationin a zebrafish contacted or treated with a test compound is compared toa control. In some examples, the control is a zebrafish (or populationof zebrafish) treated under the same conditions, but without treatmentwith the test compound. A decrease in the presence or amount of themarker of inflammation in the treated zebrafish (such as an decrease ofat least about 10%, about 20%, about 50%, about 80%, about 90%, about1.5-fold, about 2-fold, about 3-fold, about 5-fold, about 10-fold ormore) as compared to in the control indicates that the compound inhibitsimmune response or inflammation.

Bacterial strains or test compounds identified as an inhibitor of immuneresponse or inflammation may be selected for further testing. If theinhibitor is a bacterial strain or CFS from a bacterial strain,additional testing may be carried out to identify or purify one or moreanti-inflammatory compounds from the bacterial strain.

Bacterial strains that may be used in the screening methods disclosedherein (either for inoculation of germ-free zebrafish or for preparingCFS with which the zebrafish are contacted) include, but are not limitedto Aeromonas, Vibrio, Variovorax, Delftia, Acinetobacter, Shewanella,Chitinibacter, Bosea, Exiguobacterium, Carnobacterium, Ensifer, Korcuia,Comamonas, and Lactobacillus. Additional bacterial strains, such asadditional strains found in the zebrafish or mammalian gut (such as thehuman gut) can also be tested for anti-inflammatory activity in themethods disclosed herein.

A “compound” or “test compound” is any substance or any combination ofsubstances that is useful for achieving an end or result. Any compoundthat has potential (whether or not ultimately realized) to modulateimmune response or inflammation can be tested using the methods of thisdisclosure.

Exemplary compounds include, but are not limited to, peptides, such assoluble peptides, including but not limited to members of random peptidelibraries (see, e.g., Lam et al., Nature, 354:82-84, 1991; Houghten etal., Nature, 354:84-86, 1991), and combinatorial chemistry-derivedmolecular libraries made of D- and/or L-configuration amino acids,phosphopeptides (including, but not limited to, members of random orpartially degenerate, directed phosphopeptide libraries; see, e.g.,Songyang et al., Cell, 72:767-778, 1993), antibodies (including, but notlimited to, polyclonal, monoclonal, humanized, anti-idiotypic, chimericor single chain antibodies, and Fab, F(ab′)₂ and Fab expression libraryfragments, and epitope-binding fragments thereof), small organic orinorganic molecules (such as, so-called natural products or members ofchemical combinatorial libraries), molecular complexes (such as proteincomplexes), or nucleic acids (such as antisense compounds).

Appropriate compounds can be contained in libraries, for example,synthetic or natural compounds in a combinatorial library. Numerouslibraries are commercially available or can be readily produced; meansfor random and directed synthesis of a wide variety of organic compoundsand biomolecules, including expression of randomized oligonucleotides,such as antisense oligonucleotides and oligopeptides, also are known.Alternatively, libraries of natural compounds in the form of bacterial,fungal, plant and animal extracts are available or can be readilyproduced. Additionally, natural or synthetically produced libraries andcompounds are readily modified through conventional chemical, physicaland biochemical means, and may be used to produce combinatoriallibraries. Such libraries are useful for the screening of a large numberof different compounds.

In some examples, the number of neutrophils is measured by counting thenumber of neutrophils in the blood of a subject or in the gut of asubject. Methods for counting neutrophils include manual counting (forexample examining a sample (such as blood or tissue under a microscope)and counting the number of neutrophils or automated methods, such asflow cytometry. Neutrophils can be identified by staining techniques,including histological stains (such as hematoxylin and eosin),immunohistochemistry using neutrophil-specific antibodies orcombinations of antibodies (such as anti-CD11b, anti-CD68,anti-neutrophil elastase, anti-pANCA, or anti-MPO), or by detectingneutrophil-specific enzyme activity (such as chloroacetate esterasestaining). In other examples, the number of neutrophils is measuredusing a label that is expressed under the control of aneutrophil-specific promoter (such as transgenic zebrafish expressing afluorescent protein such as GFP under the control of the MPO promoter;Renshaw et al., Blood 108:3976-3978, 2006). In some examples, influx ornumbers of neutrophils is measured using light sheet microscopy (see,e.g., Baker et al., J. Microsc. 25:105-112, 2015, incorporated herein byreference), for example using light sheet microscopy to detectneutrophils expressing GFP under the control of the MPO promoter. Adecrease in the number of neutrophil cells (such as an decrease of atleast about 10%, about 20%, about 50%, about 80%, about 90%, about1.5-fold, about 2-fold, about 3-fold, about 5-fold, about 10-fold ormore) in zebrafish in the presence of one or more bacterial strains ortest compounds as compared to in the absence of the one or morebacterial strains or test compounds indicates that the compound inhibitsimmune response or inflammation.

The following examples are provided to illustrate certain particularfeatures and/or embodiments. These examples should not be construed tolimit the disclosure to the particular features or embodimentsdescribed.

Example 1 Secreted A. veronii Anti-Inflammatory Factor

This example describes identification of a secreted factor from A.veronii with anti-inflammatory activity.

Methods

All experiments performed with zebrafish were done according toprotocols approved by the University of Oregon Institutional Animal Careand Use Committee. Conventionally-raised wild-type (AB×Tu strain) andTg(BACmpx:GFP)^(il14) (referred to as mpx:GFP) (Renshaw et al., Blood108:3976-3978, 2006) were maintained as described (Westerfield, TheZebrafish Book, University of Oregon Press, Eugene, Oreg., 2000). Thempx: GFP zebrafish are transgenic for an insertion of EGFP at the MPOATG start site.

Zebrafish embryos were derived germ free (GF) as previously described(Bates et al., Dev. Biol. 297:374-386, 2006), except the fish weresoaked in 0.1% polyvinylpyrrolidone-iodine (PVP-I, Sigma-Aldrich, St.Louis, Mo.) for 2 minutes, washed three times in sterile embryo medium(EM), soaked in 0.003% bleach for 10 minutes, then washed in sterile EM.Subsequently, 15 GF embryos were transferred to sterile tissue cultureflasks with 50 mL of EM. Mono-associated zebrafish were generated byinoculating the flask 4 days post fertilization (dpf) with 10⁶ colonyforming units (CFU)/mL of bacteria. All manipulations to the GF flaskswere performed under a class II A/B3 biological safety cabinet. Theflasks were kept at 28° C. until analysis of myeloperoxidase positive(MPO+) cells.

To create an inducible expression vector for the AP protein, the AP genewas amplified using the following primers: F1882NdeI,5′-CGTACATATGATGAAAATGCACAACAAAGCGCTGC-3′ (SEQ ID NO: 3) and R1882XhoI,5′-CTGACTCGAGTTATCGCTTGTCAGCGGTGATCAG-3′ (SEQ ID NO: 4) with NdeI andXhoI restriction sites included. The PCR amplification products and thevector (pET-21b) were digested with NdeI and XhoI (New England Biolabs,Ipswich, Mass.) and ligated using T4 ligase (NEB) following themanufacturer's protocol. Subsequently, the ligated product wastransformed into BL21 E. coli. To induce AP expression, E. coli wastreated with 0.1 M IPTG in early exponential phase and was allowed togrow and produce protein for 2 hours. This resulted in a supernatantthat was dominated by AP (FIG. 8).

After A. veronii was grown over night to stationary phase and afterprotein induction in E. coli, concentrated cell-free supernatant (CFS)was prepared. The 50-mL cultures were centrifuged at 7000×g for 10minutes at 4° C. Subsequently, the supernatant was filtered through a0.22-μm sterile tube top filter (Corning Inc., NY). The sterilesupernatant was concentrated at 4° C. for 1 hour at 3000×g with acentrifugal device that has a 10 kDa weight cut off (Pall LifeSciences). The concentration of the supernatant was determined with aNanodrop and inoculated into the flasks for a final concentration of 500ng/mL.

MPO+ cell analysis was performed on 6 dpf. The mpx: GFP zebrafish wereanesthetized in Tricaine and mounted in 4% methylcellulose.Subsequently, their guts were sterilely dissected. The number ofGFP-positive cells was quantified visually for each fish.

Results

In order to identify factors secreted by zebrafish gut microbiota thatpotentially alter innate immune responses, zebrafish larvae were rearedconventionally (CV), germ-free (GF), in the presence of A. veronii, orin the presence of a mutant A. veronii strain lacking the type IIsecretion system (ΔT2SS; Maltz and Graf, Appl. Environ. Microbiol.77:597-603, 2011). One strain of A. veronii, ZF01, induced significantlymore neutrophil influx than the genetically similar A. veronii Hm21.This result suggested that A. veronii Hm21 secreted a factor thatreduced neutrophil influx in the intestine and Hm21 was selected forfurther investigation.

The type II secretion system (T2SS) is the main terminal branch of thegeneral secretion pathway and is involved in secretion of proteinsincluding proteases, cellulases, pectinases, phospholipases, lipases,and toxins. The ΔT2SS A. veronii strain has a reduced number of secretedproteins compared to strains with an intact T2SS system. Zebrafishraised in the presence of ΔT2SS A. veronii Hm21 had a greater neutrophilresponse than those raised GF or in the presence of wild-type A. veronii(FIG. 1). CFS from wild-type A. veronii rescued the low neutrophilinfiltration phenotype in zebrafish raised with ΔT2SS A. veronii (FIG.2).

Mass spectrometry of CFS from wild type and ΔT2SS A. veronii revealedsignificant increases in several secreted proteins (Table 1). CFS fromwild-type A. veronii was fractionated by ammonium sulfate precipitation,and fractions were tested for their ability to stimulate neutrophilresponse (FIG. 3). The activity was concentrated in one fraction. Thefractions were analyzed by SDS-PAGE and the active fraction was found tocontain two major bands—one of about 55 kD and one of about 35 kD (FIG.4). The molecular weight of the proteins with increased amounts inwild-type versus ΔT2SS A. veronii was considered (Table 1) to selectcandidate anti-inflammatory proteins.

TABLE 1 Molecular weight of proteins increased in WT A. veronii ascompared to ΔT2SS A. veronii MW (kD) Protein 109.316 Metalloproteasestce OS = Aeromonas veronii (strain B565) 51.919 Chitin-binding protein,carbohydrate-binding module family (CBP) 63.724 Protease OS = Aeromonasveronii (strain B565) 91.892 Putative trimethylamine-N-oxide reductase 169.583 Chitinase 130.48 Putative uncharacterized protein 103.622Collagenase family 53.921 Aeromonas virulence factor (hemolysin) 66.694Serine protease Ahe2 93.066 Chitinase A 145.483 Pullulanase 61.732 UshAprotein 107.821 Chitinase 33.386 Putative uncharacterized protein(called 1882 or AP) 79.011 Glycoside hydrolase family 18 70.456Twin-arginine translocation pathway signal 78.444 Predictedextracellular nuclease 92.107 Chitinase 92 73.3332′,3′-cyclic-nucleotide 2′-phosphodiesterase

To test the activity of candidate A. veronii proteins, AP and CBP wereeach cloned and expressed in E. coli. The E. coli genome does notcontain homologues of AP or CBP. CFS from the recombinant E. coli wasapplied to GF-reared zebrafish. Neutrophil influx was decreased by CFSfrom E. coli expressing AP; however CFS from E. coli expressing CBP hadno effect on neutrophil influx (FIG. 5).

Example 2 Effect of AP on Response to Infection

This example describes the effect of AP on response of zebrafish toVibrio infection.

Zebrafish were raised as described in Example 1, either GF ormono-associated with a Vibrio species isolated from zebrafish gut. After48 hours of Vibrio infection (inoculated at 10⁶ cfu/ml), CFS from E.coli expressing AP was inoculated in the culture at 500 ng/ml. MPOpositive cells in the gut were measured as described in Example 1.

Infection with Vibrio increased the neutrophil influx in zebrafish gutas compared to GF zebrafish (FIG. 6). Treatment of zebrafish infectedwith Vibrio with CFS from E. coli expressing anti-inflammatory proteinAP reduced neutrophil influx in response to Vibrio infection to levelscomparable to that in GF zebrafish (FIG. 6). CFS from E. coli carrying acontrol plasmid had no effect on neutrophil influx.

Example 3 Effect of AP in a Zebrafish Model of Colitis

This example describes the effect of AP in a zebrafish mutant (sox10)that is a model of colitis.

Zebrafish sox10 mutant fails to differentiate enteric neurons, resultingin a lack of rhythmic peristaltic activity (Renshaw et al., Blood108:3976-3978, 2006) and is a model for colitis. These mutants hadsignificantly higher bacterial loads than their wild-type siblings (FIG.9A). 16S rRNA profiling of the sox10 gut microbiota revealed a reduceddiversity (alpha diversity) compared to the microbiota from theirwild-type siblings (FIG. 9B), which is similar to the types of microbialdysbiosis observed in ulcerative colitis (Renshaw et al., Blood108:3976-3978, 2006). Furthermore, these mutants had a significantlyincreased level of neutrophils in their intestine (FIG. 9C), a phenotypethat was transferred to wild-type zebrafish upon inoculation ofgerm-free fish with the microbiota from sox10 fish (FIG. 9D), similar totransmissible colitis mouse models (Zenewicz et al., J. Immunol.190:5306-5312, 2013; Garrett et al., Cell 131:33-45, 2007). These datademonstrated that the sox10 fish can be used as a model for dysbiosisand transmissible intestinal inflammation. In addition, treating sox10mutants with AP significantly reduced neutrophil influx to the intestine(FIG. 10).

Example 4 Effect of AP Knockout Strain in Zebrafish

This example describes a bacterial strain that does not express AP andits effect in zebrafish.

An Aeromonas AP knockout strain was produced using homologousrecombination to replace the AP gene with a chloramphenicol resistancecassette (cm^(R)) (A. veronii Δap::cm^(R)). The cm^(R) was amplifiedfrom the pKD3 plasmid (GenBank accession number AY048742) using theprimers 1882 cm.Mid5 (5′ GCGACAGCAAGGAATAAAAACTC; SEQ ID NO: 5) and 1882cm.Mid3 (5′ CACCCCTGCCGTTAGCTGCTTAT; SEQ ID NO: 6). These primersinclude sequence that overlaps with Hm21 genome surrounding the AP genesequence. An approximately 1000 base pair region upstream and downstreamof the AP gene was amplified by PCR using the following primers:Cm1882.up3 (5′CTAAGGAGGATATTCATATGCAT; SEQ ID NO: 7), 1882.up5 (5′GATGGTCTGGGTATTGCCGTTG; SEQ ID NO: 8), cm1882.dn5 (5′CGAAGCAGCTCCAGCCTACACA; SEQ ID NO: 9), and 1882.dn3 (5′GCTGTTCGTCATCGATCGGCGC; SEQ ID NO: 10). The amplification products wereput together using the three products as a template and the 1882.up5 and1882.dn3 primers. Subsequently, the piece was ligated into the pDMS197plasmid (Edwards et al., Gene 207:149-157, 1998). The resulting plasmidwas transformed into the E. coli λpir+SM10 strain, which was used tomate at 30° C. for 4 hours with Aeromonas Hm21. Aeromonas Hm21 ΔAP wereselected by resistance to chloramphenicol and confirm by PCR.

This mutant did not have a growth defect in vitro and colonized thezebrafish to wild-type levels. In these experiments, infection ofzebrafish with an A. veronii Hm21 whose AP was knocked out (ΔAP) inducedmore inflammation than wild-type A. veronii Hm21 (FIG. 11).

Example 5 Methods of Screening for Modulators of Immune Response orInflammation

This example describes particular methods that can be used for screeningfor modulators of immune response or inflammation utilizing transgeniczebrafish that express GFP under the control of the MPO promoter. Oneskilled in the art will appreciate that methods that deviate from thesespecific methods can also be used to successfully screen for modulatorsof immune response or inflammation.

Protocol for screening anti-inflammatory protein:

Day 1: Set up mpo:GFP fish to cross naturally. Use dividers to preventegg laying until the morning.

Day 2 (0 dpf):

-   -   1. By 9:00 am, move natural crosses into tanks with fresh water        and pull dividers to allow fish to mate. Prepare antibiotic EM        to collect eggs (100 μg/mL ampicillin, 5 μg/mL kanamycin, and        250 μg/ml amphotericin B, sterile filtered). Collect eggs in        antibiotic EM and place in 30° C. incubator until they reach        shield stage.    -   2. Move embryos into sterile 50-mL beaker. Wash embryos 3× in        sterile EM. Immerse embryos in 0.1% PVP-I solution for 2        minutes. Rinse 3× in sterile EM. Transfer embryos to a new        sterile 50-mL beaker and immerse in 0.003% bleach for 20        minutes. Pour off bleach and rinse 3× in sterile EM. Transfer 15        embryos into 50-mL sterile cell culture flasks with 15-mL        sterile EM.

Day 5 (3 dpf):

-   -   1. Start overnight bacterial cultures. Start 50-mL cultures of        any of the bacteria whose CFS you want to test for        anti-inflammatory activity. Additionally start cultures that you        need to induce inflammation, for example A. veronii or Vibrio. I        estimate that a person could reasonably test 8 to 10 different        bacterial CFS preparations in one experiment.

Day 6 (4 dpf):

-   -   1. Follow CFS preparation protocol listed above.    -   2. Visually check GF fish flasks for bacteria.    -   3. Inoculate flasks with 10⁶ cfu/ml bacteria (either A. veronii        or Vibrio) and in some also include 500 ng/ml concentrated CFS.        For each experiment, include one flask with no additional        protein as a control and a GF flask as a control. Collect 1-mL        of flask water before inoculation to plate and confirm that        flasks were germ free at the start of the experiment.

Day 8 (6 dpf):

-   -   1. Check the plates with the inoculation water to ensure the        flasks were germ-free before you started.    -   2. One flask at a time, add tricaine to the fish to anesthetize        them. Rub 5% methylcellulose on a microscope slide. Use a glass        pipette to carefully pull each fish out of the flask and place        it on the prepared slide. Use the pipette to pull off any excess        EM from the slide.    -   3. Under a dissecting microscope, use dissecting needles to pull        the gut out of the fish, keeping it intact. Using a fluorescence        microscope, visualize the GFP with a 395-nm light and count the        number of neutrophils that are associated with the gut. Repeat        steps 2 and 3 for 10-15 fish per each CFS treatment.

Example 6 Testing of AP in Zebrafish Models of Disease

This example describes particular methods that can be used to test theeffect of AP on inflammation in zebrafish models of gut disease.However, one skilled in the art will appreciate that methods thatdeviate from these specific methods can also be used to successfullytest the effect of AP on inflammation in zebrafish.

Zebrafish are treated with AP (for example, purified protein or CFS fromE. coli expressing AP) and one or more markers of inflammation in thegut are determined. A reduction of one or more markers of inflammationin fish treated with AP as compared to control (untreated fish)indicates that AP decreases inflammation in the zebrafish gut.

In one example, a zebrafish model of Hirschsprung disease is used. Thesezebrafish have a mutation in a transcription factor, which results in alack of peristalsis and a significant increase in gut inflammation overWT fish. This line is crossed with mpo: GFP zebrafish. The fish areraised conventionally and treated with the AP-enriched CFS (e.g.,500-1000 ng/mL) on 4 dpf. On 6 dpf the guts are dissected and the numberof infiltrating neutrophils in the gut is counted (for example, bydetecting GFP). A reduction in neutrophil influx to the gut inAP-treated fish compared to the untreated fish indicates that thisprotein reduces inflammation in a model of Hirschsprung disease.

In another example, larval zebrafish exposed to trinitrobenzene sulfonicacid (TNBS) have impaired intestinal homeostasis and inflammation thatmodels what is observed in human inflammatory bowel disease (IBD). Totest the activity of AP in this model, conventionally raised 3 dpfmpo:GFP zebrafish are placed in groups of 15 fish in 15-mL EM and TNBSis added to a final concentration of 100 m/mL. On 4 dpf the fish aretreated with 500 ng/mL to 1000 ng/mL AP-enriched CFS from the induced E.coli expressing anti-inflammatory protein AP. On 6 dpf the guts aredissected and the number of infiltrating neutrophils in the gut iscounted (for example, by detecting GFP). A reduction in neutrophilinflux to the gut in AP-treated fish compared to the untreated fishindicates that this protein reduces inflammation in a model of IBD.

Example 7 Testing of AP in Mice

This example describes particular methods that can be used to test theeffect of AP on inflammation in mice. However, one skilled in the artwill appreciate that methods that deviate from these specific methodscan also be used to successfully test the effect of AP on inflammationin mice

Adult mice are placed on three, 3-day cycles of 3% Dextran SulfateSodium (DSS) (Whittem et al., J. Vis. Exp. 35:6-8, 2010) with seven daysof recovery between each cycle. A baseline weight for each mouse isobtained prior to DSS treatment and mice are weighed regularly duringthe experiment. As a positive control, additional mice are administeredmouse IL-1ra (Sigma), which has been shown to alleviate inflammatorysymptoms and neutrophil infiltration (reviewed in Rolig et al., Infect.Immun. 81:1382-1389, 2013). Treatment with AP is administration of50-1000 ng/ml of purified AP added to the drinking water during the DSStreatment cycles. After the final recovery period, each mouse isweighed, sacrificed, and necropsied. In necropsy, the colon is removedand the length is documented, then fixed in 4% paraformaldehyde. Samplesare embedded in paraffin, mounted, sectioned, and stained withhematoxylin and eosin for histologic analysis. Pathology is scored,including inflammation severity and epithelial cell integrity in theexperimental and control colons (for example, in a double blindfashion). The ability of AP to alleviate inflammation in the colon iscompared to exogenous mouse IL-1ra. Specific markers of inflammation arealso evaluated, for example, Ly6B.2 (neutrophils), F4/80 (macrophages),and Ki67 (proliferation). Effectiveness of AP in mice may be indicatedby decreased weight loss, increased colon length, and/or decreasedpathologic and histologic markers of inflammation compared to micetreated with DSS alone (no AP treatment).

Example 8 Method of Treating or Inhibiting Inflammation

This example describes particular methods that can be used to treat orinhibit inflammation in a subject. However, one skilled in the art willappreciate that methods that deviate from these specific methods canalso be used to successfully treat or inhibit inflammation in a subject.

Based upon the teaching disclosed herein, inflammation or aninflammatory disease can be treated or inhibited by administering aneffective amount of a composition including an Aeromonasanti-inflammatory protein, a nucleic acid encoding the protein, or apreparation including bacteria that produce the protein to a subjectwith inflammation or an inflammatory disease.

In an example, a subject with an inflammatory disease is identified andselected for treatment. For example, a subject diagnosed withinflammatory bowel disease may be selected for treatment. Followingsubject selection, an effective dose of the composition or preparationincluding the anti-inflammatory protein, nucleic acid, or bacteriadescribed above is administered to the subject. The amount of thecomposition or preparation administered to prevent, reduce, inhibit,and/or treat inflammation or an inflammatory disease depends on thesubject being treated, the severity of the disorder, and the manner ofadministration of the composition. Ideally, an effective amount of anagent is the amount sufficient to prevent, reduce, and/or inhibit,and/or treat the condition (e.g., inflammatory disease) in a subjectwithout causing substantial adverse effects in the subject.

In one specific example, an anti-inflammatory protein (such as SEQ IDNO: 1) or a fragment thereof (such as amino acids 148-176 of SEQ IDNO: 1) is administered to a subject. For example, an anti-inflammatoryprotein is administered to a subject at about 1 mg to 1 g daily. Inanother example, an anti-inflammatory protein is administered at about 1mg to 1 g biweekly or weekly. In further examples, a nucleic acidencoding an anti-inflammatory protein (such as SEQ ID NO: 2) isadministered to a subject at about 1 mg to 1 g daily, biweekly, orweekly. An appropriate dose can be selected by a skilled clinician basedon the subject, the condition being treated and other factors.

Subjects are monitored by methods known to those skilled in the art todetermine responsiveness of the inflammation or inflammatory diseasetreatment. For example, if the condition is inflammatory bowel disease,the symptoms of the subject are monitored, for example using the Crohn'sDisease Activity Index or the Harvey-Bradshaw Index. It is contemplatedthat additional agents can be administered, such as additionalanti-inflammatory agents in combination with or following treatment withthe Aeromonas anti-inflammatory protein.

Example 9 Identification of Calycin-Like Domains in AimA Materials andMethods

Protein Purification and Crystallization:

AimA gene was PCR amplified from gDNA excluding the N-terminal (22 aminoacid) secretion signal and cloned into pET21b using NdeI and XhoIrestriction sites. The resultant gene expressed well in E. coli BL21 asa C-terminal 6× His tagged protein of 300 amino acids long (includingHis tag and linker).

The E. coli culture was grown at 37° C. until OD600 0.4-0.6, then movedto 30° C. and induced with 1 mM IPTG for 3-4 hr. All subsequent stepswere performed at 4° C. One to two liters of pelleted E. coli cells werelysed in lysis buffer (50 mM HEPES pH 7.9, 300 mM NaCl, 10 mM imidazole,and 5 mM BME), sonicated, and debris pelleted. The supernatant waswashed over 5 mL Ni-NTA resin in a gravity column that was pre-washedwith lysis buffer. The resin was washed with 15× bed volume of lysisbuffer, then 10× bed volume of lysis buffer with 30 mM imidazole, 10×bed volume of lysis buffer with 50 mM imidazole and finally eluted with3×-5× bed volume of lysis buffer plus 100-300 mM imidazole. The highabsorbance (280 nm wavelength) fractions were pooled and dialyzedovernight into 150 mM NaCl, 50 mM HEPES pH 7.9, and 5 mM BME,concentrated, and flash frozen in liquid nitrogen.

Purified AimA with C-terminal 6× His tag was concentrated to 10.9 mg/mLand set up in hanging drops as 1 μL protein:1 μL well solution at roomtemperature. AimA crystallized in thick hexagons in 3.5 M sodiumformate, 75 mM NaCl, 25 mM HEPES pH 7.9, and 2.5 mM BME. One to twoweeks after the crystals grew, they were transferred to wells containing3.8 M sodium formate to toughen them up for approximately one week. Theheavy atom derivative crystals were then transferred to drops with 3.8 Msodium formate, 0.5 M NaI (for iodide data set), and 15% glycerol (as acryoprotectant) for several hours before being scooped and flash frozenin liquid nitrogen for data collection at the Advanced Light Source inBerkley, Calif., beamline 5.0.2 using the Pilatus detector at awavelength of 1.0 Å. The native crystals were transferred to 3.8M sodiumformate and 15% PEG 200 briefly, then flash frozen in liquid nitrogenfor data collection as described for the iodide soaked crystals.

Structure Determination of AimA

Data Processing: The heavy atom derivative was solved by thesingle-wavelength anomalous diffraction (SAD) method from a singlecrystal derivatized with I⁻, with data collected at wavelength λ=1 Å.The data set was integrated and scaled to resolution 2.7 Å using HKL3000(Minor et al., Acta Crystallogr Sect D Biol Crystallogr. 2006;62:859-866) with the merging analysis indicating the P622 space group.Although data were isotropic, diffraction spots were smeared in a mannerindicating the presence of order-disorder. In addition, the scalingB-factor increase of ˜40 Å², which is equivalent to a dose of ˜40 MGy,indicated severe radiation damage. Therefore, it was necessary to applythe ‘automatic corrections’ computational procedure to optimize theerror model (Borek et al., Acta Crystallogr Sect D Biol Crystallogr.2010; 66:426-36; Borek et al., J Synchrotron Radiat. 2013; 20:37-48;Borek et al., J Synchrotron Radiat. 2007; 14:24-33), and this wasessential for the success of the experimental phasing described below.

The estimated level of anomalous signal was ˜3.6% of the nativeintensity. The search for heavy atom positions was performed to aresolution of 3.7 Å. The 30 positions of I⁻ were identified usingSHELXC/D (Sheldrick, Acta Crystallogr Sect D Biol Crystallogr. 2008;64:112-122), run within HKL3000, with correlation coefficients:CC_(All)=41.4%, CC_(Weak)=16.1%. The handedness of the best solution wasdetermined with SHELXE. The heavy atom positions were refined to 2.7 Åwith MLPHARE (Otwinowski, Pap Present CCP4 Study Weekend. 1991) with thefinal Figure of Merit (FOM) reaching 0.14 for all observations. Solventflattening was performed by DM (Cowtan et al., Acta Crystallogr Sect DBiol Crystallogr. 1998; 54: 487-493). The procedure produced aninterpretable electron density map that was used for iterative automaticmodel building with BUCCANEER, Coot and REFMAC (Cowtan, Acta CrystallogrSect D Biol Crystallogr. 2006; 62:1002-1011; Emsley et al., ActaCrystallogr Sect D Biol Crystallogr. 2004; 60:2126-2132; Murshudov etal., Acta Crystallogr Sect D Biol Crystallogr. 1997; 53:240-255;Murshudov et al., Acta Crystallogr Sect D Biol Crystallogr. 1999;55:247-255)—all run within HKL3000 with ‘HKL Builder’ option. Thatprocedure resulted in 100% of the model being built with 90% of the sidechains docked. At this point, the R and R-free factors were ˜27% and˜35%, respectively.

Two native AimA datasets from separate crystals were indexed andintegrated with iMosflm 7.2.1 (Battye et al., Acta Crystallogr D BiolCrystallogr. 2011; 67:271-281) and scaled using SCALA (CollaborativeComputational Project N 4, Acta Crystallogr D Biol Crystallogr. 1994;50:760-763). The two datasets were found to be isomorphous, and werecombined using POINTLESS (Collaborative Computational Project N 4, ActaCrystallogr D Biol Crystallogr. 1994; 50:760-763). The high-resolutioncutoff was determined by the method of Karplus & Diederichs (Science2012; 336:1030-1033) using a CC_(1/2) of >0.3 and completeness of >50%in the highest resolution shell. This method has been utilized innumerous other studies (Perkins et al., Structure 2016; 24: 1668-1678;Evans et al., Acta Crystallogr D Biol Crystallogr. 2013; 69:1204-1214;Kern et al., Science 2013; 340: 491-495) and has been cited over 900times since its publication. Using these criteria, the correlationbetween two halves of the data are used to determine the point at whichsignal falls away into noise (Evans et al., Acta Crystallogr D BiolCrystallogr. 2013; 69:1204-1214), and R_(merg) values can rise to valuesmuch higher than what has traditionally been thought of as allowable.Using this strategy we were able to extend the resolution from 2.9 Å(where the data would have been cut based on R_(merg) ˜0.6) to 2.3 Å. Tofurther test the validity of using this noisy high-resolution data torefine the model, a series of paired refinements were conducted (Karplus& Diederichs, Science 2012; 336:1030-1033). The model was first refinedusing data out to 2.9, 2.7, 2.5, or 2.3 Å and then, since R values areonly comparable when calculated at the same resolution (Karplus &Diederichs, Science 2012; 336:1030-1033), R and R_(free) were calculatedfor each refined model at 2.9 Å (FIG. 12). The extra resolution improvedboth R (higher value) and R_(free) (lower value), showing that the modelis improved in predictive quality and is less overfit using the extendedresolution cutoff. In this case CC_(1/2) remains quite high at 0.9 inthe high-resolution shell, and the <I/σ> at 1.4 is not far below atraditional cutoff of 2.0. Data statistics are summarized in Table 2.

Refinement:

Manual model building was performed using Coot 0.8.1.6 (Emsley et al.,Acta Crystallogr Sect D Biol Crystallogr. 2004; 60:2126-2132) andrefinement was carried out using PHENIX 1.12-2829 (Adams et al., ActaCrystallogr Sect D Biol Crystallogr. 2010; 66:213-221). Initial rigidbody refinement resulted in R/R_(free) values of 26.5/28.3%. Using theextended resolution improved the electron density maps and allowedplacement of additional water molecules, two formate molecules (presentat 3.5 M in the crystallization buffer), N-terminal residues 1-8, and analternate chain path for residues 153-165, improving R/R_(free) to20.9/24.8%. Residues 180-181 are at the tip of a disordered loop andwere not modeled, and residues 293-294 and the C-terminal His-tag beyondit are not visible in the electron density. Electron density is weak inseveral regions including the N-terminus and several loops, but thechain path was clear enough to build at least the backbone atoms forthese residues. In late stages of refinement, TLS was implemented usingone group per chain, dropping R/R_(free) to 17.9/20.9%. B-factor weightswere optimized in the final refinement step, yielding final R/R_(free)of 17.2/20.4% for the final AimA model (Table 2).

TABLE 2 Data Collection and Refinement Statistics for Model IodideNative Data Collection Space group P622 P622 Unit cell a, b, c (Å) 161.4161.4 66.6 160.5 160.5 66.2 Alpha, beta, gamma (degrees) 90 90 120 90 90120 Resolution (Å) 50.0-2.7 (2.75- 41.1-2.30 2.70) Completeness (%) 100(100) 100 (100) No. unique reflections 14772 (711)  22818 (3244)Multiplicity 37.7 (38.1) 70.2 (71.6) <I/sigma> 44.2 (3.5)  16.1 (1.4) CC1/2 1 0.861 1.0 (0.9) CC1/2 anomolous 1 0.873 R merge (%) 19.6 (486) 19.1 (574)  Refinement R work (%) 17.2 R free (%) 20.4 No. of moleculesin the 1 asymmetric unit No. protein residues 290 No. of waters 69 rmsdfor lengths (Å) 0.008 rmsd for angles (deg) 1.1 Ramachandran plot (%)Preferred 96.2 Allowed 3.4 Outliers 0.4 Avg. B factor (Å{circumflex over( )}2) Mainchain^(A) 81 Waters 75 ^(A)Several loop regions display highmobility but have been modeled due to a visible chain path in theelectron density, resulting in an increase in the average observedB-factors of the main chain

Results

Analysis of the amino acid sequence of AimA with the N terminal aminoacid secretion signal removed revealed a lack of sequence identity withknown domains or structurally characterized proteins and thereforeoffered little insight into the structure or function of AimA. To gaininsight into the mechanism of AimA, we constructed a recombinant proteinwith a C-terminal His-tag. His-tagged AimA produced in E. coli waspurified and crystallized to determine the molecular structure using aheavy atom derivative and Single-wavelength Anomalous Dispersion (SAD)phasing to a resolution of 2.3 Å (Table 2). The structure of AimArevealed two domains connected by a short linker (FIGS. 13A and 13B).β-strands dominate each domain, with the carboxy terminal (C-term)domain forming a complete β-barrel and the amino terminal (N-term)domain containing a curved β-sheet. Structural homology searches of fulllength AimA against all Protein Data Bank-deposited structures usingPDBeFold resulted in structures that aligned to only one domain or theother, with the majority aligning with the C-term domain (Krissinel etal., Acta Crystallogr Sect D Biol Crystallogr; 2004; 60:2256-2268;Berman et al., Nucleic Acids Res. 2000; 28:235-242). Therefore, weperformed structural homology searches against each domain separately,which revealed that both domains had similarity to proteins in thecalycin superfamily (Table 3 and FIGS. 14A-14B). The calycin superfamilyis found across all domains of life and includes lipocalins, fatty acidbinding proteins, and avidins. This superfamily is defined by ananti-parallel β-barrel with a repeated+1 topology (Flower, Biochem J.1996; 318 (Pt 1: 1-14). Notably, the calycin superfamily is known forstructural conservation without high amino acid sequence conservation(Flower, Biochem J. 1996; 318 (Pt 1: 1-14); Lakshmi et al., PLoS One.2015; 10:1-18), which helps explain the lack of sequence homology forAimA. The N-term domain of AimA has an incomplete β-barrel, butmaintains some structural homology to streptavidin. Streptavidin bindsbiotin tightly, but AimA does not appear to bind biotin (FIGS. 14C-14D).The C-term domain of AimA has structural homology both to avidins andlipocalins (Table 3). Some lipocalin proteins, like human lipocalin-2,or NGAL, are known to influence neutrophil behavior (Moschen et al.,Trends Endocrinol Metab. 2017; 28:3880397).

TABLE 3 Structural homology hits to each AimA domain PDB AimA domainProtein Organism ID Q score RMSD Amino terminal Engineered Streptomycesavidinii 1kl3 0.18 2.69 (19 total hits) Streptavidin Avidin Gallusgallus 1lel 0.16 3.56 Zebavidin Danio rerio 4bj8 0.15 3.15 Carboxyterminal Avidin Gallus gallus 1lel 0.32 2.58 (220 total hits) ZebavidinDanio rerio 4bj8 0.32 2.58 Lipocalin Streptococcus 5cyb 0.29 2.28lipoprotein pneumonia Lipoprotein Treponema pallidum 4u3q 0.26 2.09Streptavidin Streptomyces avidinii 2izf 0.26 2.77 Retinol binding Homosapiens 4o9s 0.18 2.89 protein 4 Lipocalin-2 (LCN2, Homo sapiens 3i0a0.16 3.07 NGAL) Engineered Streptomyces avidinii 1kl3 0.18 2.69Streptavidin Q score RMSD Protein families range range Avidins 0.32-0.172.58-2.87 Bacterial lipocalins 0.29-0.21 2.28-2.85 Non-bacteriallipocalins 0.26-0.16 2.09-3.07

Example 10 Effect of AimA in a Zebrafish Model of Inflammation Methods

Soysaponin (Sigma-Aldrich, St. Louis, Mo.) was mixed with Zieglers fishfood at a concentration of 0.3%. Ten CV zebrafish were maintained 10 mLEM in 60×15 mm petri dishes. Larval fish were fed once daily from 4 dpfto 6 dpf. During each feeding, the larvae had access to the food for 3-4hours before being washed into fresh EM. For experiments with mLCN2,recombinant mouse LCN2 (Biolegend) was added to the fish EM at aconcentration of 100 ng/mL after the soysaponin feeding on 4 dpf and 5dpf after the fish were moved into fresh EM.

Results

To test whether AimA may interact directly with the host, we tested AimAfunction in a general model of intestinal inflammation, the zebrafishmodel of soysaponin-induced inflammation. Farmed fish, such as salmonand carp, fed soybean meal as a protein source are known to developintestinal inflammation, and zebrafish are a good model of thisirritation (Hedrera et al., PLoS One. 2013; 8:1-10). We fedconventionally raised zebrafish larvae Zeiglers fish food with 0.3%soysaponin from 4 dpf to 6 dpf and saw a significant increase in thenumber of intestinal neutrophils in response to the soysaponin, asexpected (FIG. 15A). When we treated the fish with 100 ng/ml purifiedAimA from 4 dpf to 6 dpf concurrently with soysaponin, AimA preventedthe increase in neutrophil influx in response to soysaponin (FIG. 15A).This result may suggest that AimA interacts directly with the hostimmune system, which makes AimA a good candidate for a therapeuticbioactive protein that reduces host inflammation.

Because AimA reduces neutrophil influx in a model of intestinalinflammation and the C-term domain has structural homology to lipocalinproteins (FIGS. 4, 5A, and 8; Table 3), we hypothesized that theneutrophil reducing capacity of AimA was related to its lipocalin-likestructure. Lipocalins are defined by three key structurally conservedregions (SCR1, SCR2, SCR3); the most conserved region is SCR1, which isconserved across kernel and outlier lipocalins and contains four keyresidues (FIG. 15B) (Flower, Biochem J. 1996; 318 (Pt 1: 1-14); Lakshmiet al., PLoS One. 2015; 10:1-18). The SCR1 in the C-term domain of AimAstructurally overlaps with the SCR1 of mouse lipocalin-2 (mLCN2) (FIG.15B). Thus, we asked whether the addition of mLCN2 protein would hinderthe capacity of AimA to reduce the neutrophil response to soysaponin.The addition of mLCN2 concurrently with soysaponin did not influence theneutrophil response to soysaponin (FIG. 15C); however, addition of mLCN2in conjunction with AimA prevented the protective effect of AimA againstsoysaponin-induced inflammation, suggesting that AimA may bind mLCN2,compete for the same host receptor, or act in a competing pathway.

Both the C- and N-terminal domains of AimA have structural homology toproteins in the calycin superfamily, they share 16% amino acid identity,and in a structural overlay between the two domains we find somestructural conservation (FIG. 16A and FIG. 17A). Human lipocalin-2 canexist both as a monomer and a homodimer, and while the functionaldistinction between the two forms is unknown, the homodimer is the majormolecular form secreted by neutrophils (Cai et al., Clin J Am SocNephrol. 2010; 5:2229-2235). Because human lipocalin-2 exists as both amonomer and homodimer, and the two domains of AimA each have alipocalin-like fold, we asked if each domain alone was sufficient toalter the intestinal neutrophil response. The individual domains werenot as soluble as full-length AimA, but we were able to crudely purifyeach domain with an N-terminal His-tag. Concurrently with soysaponin, weadded approximately 100 ng/ml of the domain of interest to zebrafishfrom 4 to 6 dpf and found that both the N- and C-term domains weresufficient to reduce neutrophil response in the soy model of intestinalinflammation (FIG. 16B).

An in depth analysis of the structural overlay between the N- and C-termdomains revealed that seven out of eight β-strands in the barrels alignwell; however, only seven total residues are in analogous positionsacross the two domains (FIGS. 17B and 17C). Of these seven residues,two—Val 60/201 and Thr 117/265—stand out as possible candidates tointeract with a hydrophobic ligand that binds inside the barrel cavity.The other five residues may overlap by coincidence or they may bepositioned to interact with a promiscuous protein or ligand partner.Furthermore, given the overall structural similarity between the N- andC-term domains, it is possible that critical residues are in a flexibleloop region that could become structured upon binding (FIG. 16A, FIGS.17A-17C). Interestingly, both AimA domains have comparable structuralsimilarity with mLCN2 (FIG. 16C). In all three domains, the majority ofthe β-strands in the barrels overlap and there is a similar cleft insidethe barrels, which suggests these domains could interact with the samereceptor or ligand (FIG. 16C). These insights into the potentialmolecular mechanism of AimA could not have been achieved with sequencealone.

Example 11 Effect of AimA on Aeromonas Fitness

With an understanding that AimA controls the host neutrophil response,we next asked whether the activity of AimA also increases Aeromonasfitness, thus facilitating the establishment of a mutualisticrelationship with the host. We began by asking how prevalent AimA wasacross bacterial genomes. Knowing that proteins in the calycinsuperfamily have low sequence conservation, we were not surprised tofind AimA homologues by sequence similarity only within the Aeromonasgenus (FIGS. 18A and 18B). These homologues ranged from 27% to 100% inamino acid sequence conservation. Some species of Aeromonas, includingA. veronii strain Hm21 (Table 4), have both AimA and a second copy,which we named AimB. AimB is distantly related to AimA by amino acidsequence conservation (27%), yet an Iterative Threading ASSEmblyRefinement (I-TASSER) generated model of the structure of AimB overlaysdirectly on the structure of AimA (FIG. 19A) (Yang et al., Nat Methods.2014; 12:7-8; Roy et al., Nat Protoc. 2011; 5:725-738; Zhang, BMCBioinformatics. 2008; 9:40). This is consistent with the low sequenceconservation but high structural conservation of proteins within thecalycin superfamily. We additionally found an almost identical homologue(99%) to AimA in a zebrafish commensal Aeromonas isolate, ZOR0001,referred to here as ZF Aer (Table 4) (Stephens et al., ISME J. 2015;10).

TABLE 4 Strain table Ref. or Strain Characteristics source AbbreviationHm21S Parent strain, Sm^(R) Graf, 1999¹ Aer HE-1095 Hm21S::interruptedexeM mTn5 Km^(R) Sm^(R) Graf, 2011² Aer ΔT2 HEC-1344 HE-1095::Tn7containing Tp^(R) exeMN + promoter Graf, 2011² Aer ΔT2C region ASRC7Hm21S aimA::cm^(R) Aer ΔaimA ASRD5 Hm21S ΔaimB Aer ΔaimB ASRD4 Hm21SaimA::cm^(R); ΔaimB Aer ΔAΔB ZOR0001 Zebrafish Aeromonas isolateStephens³ ZF Aer ASRC9 ZOR0001 aimA::cmR ZF Aer ΔaimA ¹Graf, Infect.Immun. 67: 1-7, 1999 ²Maltz and Graf, Appl. Environ. Microbiol. 77:597-603, 2011 ³Stephens et al., ISME J. 10: 644-654, 2016

To determine whether the bioactive protein AimA and its homolog AimBbenefit Aeromonas, we constructed deletion strains of each geneindividually and of both genes in A. veronii strain Hm21 (Aer ΔaimA, AerΔaimB, and Aer ΔAΔB), and an AimA deletion in the ZF Aer background (ZFAer ΔaimA). All of these mutants displayed normal growth in vitro (FIG.18B). Purified AimA reduces the intestinal neutrophil response, thus wehypothesized that the deletion strains would have a greater capacity toinduce a neutrophil response. To test our hypothesis, we mono-associatedeach of these strains in zebrafish from 4 to 7 dpf and quantified bothintestinal neutrophil number and bacterial colonization level on 7 dpf.We found that in A. veronii strain Hm21, which has both AimA and AimB,neither single deletion was different from wild type in either hostneutrophil response (FIG. 19B) or bacterial colonization (FIG. 19C).However, the double mutant that lacks both AimA and AimB induced asignificantly greater intestinal neutrophil response than the wild type(FIG. 19B) and suffered a significant colonization defect (FIG. 19C),suggesting that AimA and AimB have redundant functions. Further, thephenotypes observed in Aer ΔAΔB can be rescued in trans by addingpurified AimA protein at a concentration of 100 ng/mL to the flask waterwith mono-associated zebrafish from 4 to 7 dpf (FIGS. 19B and 19C). Wewere able to replicate these phenotypes in ZF Aer ΔaimA strain andrescue them by adding purified AimA (FIGS. 19D and 19E). These resultsalso reveal that in the absence of Aim proteins, fewer Aeromonas cellsare required to induce a larger neutrophil response, suggesting thateach ΔAΔB bacterial cell has a higher per capita effect on neutrophilinflux than wild-type Aeromonas.

Example 12 Effect of AimA on Host Survival

To induce sepsis, CV zebrafish were treated with 600 μg/mL LPS(Sigma-Aldrich, St. Louis, Mo.) on 5 dpf and monitored for survival forthe following 2 days. For experiments with AimA, AimA was added at 100ng/ml on 4 dpf.

In the absence of Aim proteins, Aer ΔAΔB infection had both reducedcolonization and induces an increased intestinal neutrophil response,which suggests that Aer ΔAΔB has a higher per capita effect than thewild-type Aeromonas strain. We calculated the number of neutrophils thatrespond to 10⁴ colonized bacteria, and discovered that Aer ΔAΔB recruitsnearly twice the number of neutrophils than the wild-type strain, onaverage, for the same number of bacteria (FIG. 20A). This demonstratesthat the Aim proteins may function, in part, to reduce the immunestimulation potential of Aeromonas, allowing Aeromonas to conceal theirhigh colonization numbers from the host. Thus, AimA allows the bacteriato reach higher colonization density without a detriment to the host.

Knowing that loss of the Aim proteins resulted in both a significantlyhigher per capita effect and a significantly increased intestinalneutrophil response, we asked if the increased neutrophil response ledto more serious health problems. Thus, as a representation of overallfish health, we monitored mono-associated fish for their survival rateover 72 hours. By 72 hours, the survival rate of wild-type Aer was 92%(n=163). We observed a significant decline in the survival of Aer ΔaimA(n=139), Aer ΔaimB (n=174), and Aer ΔAΔB (n=148), whose survival rateswere 64%, 73%, and 55%, respectively (FIG. 20B). This decreased survivalrate was rescued back to 90% by the presence of purified AimA (n=60;FIG. 20C). These data demonstrate that the Aim proteins act to promoteboth bacterial colonization and host survival, identifying AimA as a keymediator of host-bacterial mutualism.

We tested whether the ability of AimA to control the neutrophil responsewas connected to the decreased survival rate by inoculating myd88^(−/−)transgenic fish with wild-type Aeromonas or Aer ΔAΔB. myd88^(−/−) fishlack the adaptor protein Myd88 that is used by almost all toll-likereceptors (TLRs) to activate pro-inflammatory transcription pathways(Larsson et al., Gut. 2011; doi:10.1136/gutjnl-2011-301104); the lack ofMyd88 results in fish with a severely attenuated intestinal neutrophilresponse, such that their intestinal neutrophil response is notdistinguishable from germ-free wild-type zebrafish (Bates et al., CellHost Microbe. 2007; 2:371-82; Burns et al., Proc Natl Acad Sci. 2017;201702511. doi:10.1073/pnas.1702511114) (FIG. 20C). However, myd88^(−/−)fish inoculated with Aer ΔAΔB do not die at a higher rate than thoseinoculated with wild-type Aeromonas (FIG. 20D), suggesting that theincreased neutrophil response to Aer ΔAΔB is connected to the decreasedsurvival rate. We additionally found that not only do Aer ΔAΔB notexperience a colonization defect in myd88^(−/−) fish, the colonizationlevel of both Aer ΔAΔB and wild-type Aer increased significantly in themyd88^(−/−) fish compared to wild-type fish (FIG. 20E). These resultssuggest that the decreased colonization of Aer ΔAΔB in wild-type fish isdue to the increased neutrophil response and that the neutrophilresponse functions, in part, to control the colonization density ofcommensal bacteria.

Given the increase in bacterial colonization and fish death in themyd88^(−/−) fish, regardless of the colonizing strain, we hypothesizedthat these fish may be dying of sepsis as a result of bacterialovergrowth. Thus we asked whether AimA could delay death as a result ofLPS exposure, a model of bacterial sepsis in zebrafish (Philip et al,Mol Med. 2017; 23:1). To test this, we treated fish with 100 ng/mL AimAon 4 dpf then with 600 μg/mL LPS on 5 dpf and tracked their survivalover the subsequent 60 hours. Indeed, the median survival time post LPStreatment was 36 hours, which was extended to 48 hours in the presenceof AimA (FIG. 20F). Thus, AimA significantly extends the survival of LPStreated fish.

Example 13 Method of Treating or Inhibiting Sepsis or Septic Shock

This example describes particular methods that can be used to treat orinhibit sepsis or septic shock in a subject. However, one skilled in theart will appreciate that methods that deviate from these specificmethods can also be used to successfully treat or inhibit sepsis orseptic shock in a subject.

Based upon the teaching disclosed herein, sepsis or septic shock can betreated or inhibited by administering an effective amount of acomposition including an Aeromonas anti-inflammatory protein or portionthereof, a nucleic acid encoding the protein or portion thereof, or apreparation including bacteria that produce the protein or portionthereof, to a subject with sepsis or septic shock or suspected to havesepsis or septic shock.

In an example, a subject with sepsis or septic shock or suspected tohave sepsis or septic shock is identified and selected for treatment.Following subject selection, an effective dose of the composition orpreparation including the anti-inflammatory protein, nucleic acid, orbacteria described above is administered to the subject. The amount ofthe composition or preparation administered to prevent, reduce, inhibit,and/or treat sepsis or septic shock depends on the subject beingtreated, the severity of the disorder, and the manner of administrationof the composition. Ideally, an effective amount of an agent is theamount sufficient to prevent, reduce, and/or inhibit, and/or treatsepsis or septic shock in the subject without causing substantialadverse effects in the subject.

In one specific example, an anti-inflammatory protein (such as SEQ IDNO: 1 or SEQ ID NO: 11) or a fragment thereof (such as amino acids1-185, 23-185, and/or 192-313 of SEQ ID NO: 1, or amino acids 1-188,21-188, and/or 189-330 or SEQ ID NO: 11) is administered to a subject.For example, an anti-inflammatory protein is administered to a subjectat about 1 mg to 1 g daily. In another example, an anti-inflammatoryprotein is administered at about 1 mg to 1 g biweekly or weekly. Infurther examples, a nucleic acid encoding an anti-inflammatory protein(such as SEQ ID NO: 2 or SEQ ID NO: 17) or a fragment thereof (such asnucleotides 1-555, 67-555, and/or 574-939 of SEQ ID NO: 2 or nucleotides1-564, 61-564, and/or 565-990 of SEQ ID NO: 17) is administered to asubject at about 1 mg to 1 g daily, biweekly, or weekly. An appropriatedose can be selected by a skilled clinician based on the subject, thecondition being treated and other factors.

Subjects are monitored by methods known to those skilled in the art todetermine responsiveness of the sepsis or septic shock to treatment.Additional agents can be administered, such as antibiotics,vasopressors, and/or intravenous fluids, in combination with orfollowing treatment with the Aeromonas anti-inflammatory protein.

In view of the many possible embodiments to which the principles of thedisclosure may be applied, it should be recognized that the illustratedembodiments are only examples and should not be taken as limiting thescope of the invention. Rather, the scope of the invention is defined bythe following claims. We therefore claim as our invention all that comeswithin the scope and spirit of these claims.

We claim:
 1. An isolated polypeptide comprising: an amino acid sequencehaving at least 80% or at least 90% sequence identity to the amino acidsequence of SEQ ID NO: 11; an amino acid sequence 130-190 amino acids inlength and having at least 80% identity to amino acids 1-188 of SEQ IDNO: 11, amino acids 21-188 of SEQ ID NO: 11, or amino acids 189-330 ofSEQ ID NO: 11; an amino acid sequence 130-190 amino acids in length andhaving at least 80% identity to amino acids 1-185 of SEQ ID NO: 1, aminoacids 23-185 of SEQ ID NO: 1, or amino acids 192-313 of SEQ ID NO:
 1. 2.The isolated polypeptide of claim 1, wherein the polypeptide comprisesor consists of: the amino acid sequence of SEQ ID NO: 11; an amino acidsequence 130-190 amino acids in length and comprising amino acids 1-188of SEQ ID NO: 11, amino acids 21-188 of SEQ ID NO: 11, or amino acids189-330 of SEQ ID NO: 11; an amino acid sequence 120-180 amino acids inlength and comprising amino acids 1-185 of SEQ ID NO: 1, amino acids23-185 of SEQ ID NO: 1, or amino acids 192-313 of SEQ ID NO:
 1. 3. Theisolated polypeptide of claim 1, wherein the polypeptide is encoded by:a nucleic acid comprising a nucleotide sequence at least 80% identicalto the nucleic acid sequence set forth as SEQ ID NO: 17; a nucleic acid390-570 nucleotides in length and having at least 80% identity tonucleotides 1-564 of SEQ ID NO: 17, nucleotides 61-564 of SEQ ID NO: 17,or nucleotides 565-990 of SEQ ID NO: 17; a nucleic acid 360-540nucleotides in length and having at least 80% identity to nucleotides1-555 of SEQ ID NO: 2, nucleotides 67-555 of SEQ ID NO: 2, ornucleotides 574-939 of SEQ ID NO:
 2. 4. The isolated polypeptide ofclaim 3, wherein the polypeptide is encoded by: a nucleic acidcomprising or consisting of the nucleic acid sequence of SEQ ID NO: 17;a nucleic acid 390-570 nucleotides in length and comprising nucleotides1-564 of SEQ ID NO: 17, nucleotides 61-564 of SEQ ID NO: 17, ornucleotides 565-990 of SEQ ID NO: 17; a nucleic acid 390-570 nucleotidesin length and comprising nucleotides 1-555 of SEQ ID NO: 2, nucleotides67-555 of SEQ ID NO: 2, or nucleotides 574-939 of SEQ ID NO:
 2. 5. Anisolated nucleic acid, comprising: a nucleic acid comprising anucleotide sequence at least 80% identical to the nucleic acid sequenceset forth as SEQ ID NO: 17; a nucleic acid 390-570 nucleotides in lengthand having at least 80% identity to nucleotides 1-564 of SEQ ID NO: 17,nucleotides 61-564 of SEQ ID NO: 17, or nucleotides 565-990 of SEQ IDNO: 17; a nucleic acid 360-540 nucleotides in length and having at least80% identity to nucleotides 1-555 of SEQ ID NO: 2, nucleotides 67-555 ofSEQ ID NO: 2, or nucleotides 574-939 of SEQ ID NO:
 2. 6. The isolatednucleic acid molecule of claim 5, comprising or consisting of: thenucleic acid sequence of SEQ ID NO: 17; a nucleic acid 390-570nucleotides in length and comprising or consisting of nucleotides 1-555of SEQ ID NO: 2, nucleotides 67-555 of SEQ ID NO: 2, or nucleotides574-939 of SEQ ID NO: 17; a nucleic acid 390-570 nucleotides in lengthand comprising or consisting of nucleotides 1-555 of SEQ ID NO: 2,nucleotides 67-555 of SEQ ID NO: 2, or nucleotides 574-939 of SEQ ID NO:2.
 7. A recombinant vector comprising the polynucleotide of claim 5,operably linked to a heterologous promoter.
 8. The recombinant vector ofclaim 7, wherein the heterologous promoter comprises a promoter from E.coli, a viral promoter, or a mammalian promoter.
 9. A cell comprisingthe recombinant vector of claim
 7. 10. A transformed cell comprising thepolynucleotide of claim 5, operably linked to a heterologous promoter.11. The transformed cell of claim 10, wherein the heterologous promotercomprises a promoter from E. coli, a viral promoter, or a mammalianpromoter.
 12. A method of treating or inhibiting inflammation and/ortreating or inhibiting sepsis or septic shock in a subject, comprisingadministering to the subject the polypeptide of claim
 1. 13. The methodof claim 12, wherein the inflammation in the subject comprises aninflammatory disease.
 14. The method of claim 13, wherein theinflammatory disease comprises rheumatoid arthritis, osteoarthritis,inflammatory lung disease, inflammatory bowel disease, Hirschsprung'sassociated enterocolitis, pelvic inflammatory disease, periodontaldisease, polymyalgia rheumatica, atherosclerosis, systemic lupuserythematosus, systemic sclerosis, Sjogren's Syndrome, asthma, allergicrhinitis, psoriasis, irritable bowel syndrome, necrotizingenterocolitis, or atopy.
 15. The method of claim 12, wherein the amountof the polypeptide administered to the subject is about 1 mg to about 5g.
 16. The method of claim 12, wherein the effective amount of theprotein is administered to the subject daily, weekly, or monthly. 17.The method of claim 12, further comprising administering one or moreadditional anti-inflammatory therapies to the subject with inflammationor administering one or more of antibiotics, vasopressors, orintravenous fluids to the subject with sepsis or septic shock.
 18. Amethod of treating sepsis or septic shock in a subject, comprisingadministering to the subject a polypeptide comprising an amino acidsequence having at least 80% or at least 90% sequence identity to theamino acid sequence of SEQ ID NO:
 1. 19. The method of claim 18, whereinthe polypeptide comprises or consists of the amino acid sequence of SEQID NO: 1 or amino acids 23-313 of SEQ ID NO:
 1. 20. The method of claim18, further comprising administering one or more of antibiotics,vasopressors, or intravenous fluids to the subject.